Starting phenix.real_space_refine on Tue Jun 24 07:17:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yn0_33949/06_2025/7yn0_33949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yn0_33949/06_2025/7yn0_33949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yn0_33949/06_2025/7yn0_33949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yn0_33949/06_2025/7yn0_33949.map" model { file = "/net/cci-nas-00/data/ceres_data/7yn0_33949/06_2025/7yn0_33949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yn0_33949/06_2025/7yn0_33949.cif" } resolution = 4.1 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= -0.006 sd= 0.150 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 153 5.16 5 C 17682 2.51 5 N 4521 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27912 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 16.89, per 1000 atoms: 0.61 Number of scatterers: 27912 At special positions: 0 Unit cell: (155.1, 145.2, 156.2, 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 153 16.00 O 5556 8.00 N 4521 7.00 C 17682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG R 1 " - " FUC R 3 " NAG-ASN " NAG A1401 " - " ASN A 104 " " NAG A1402 " - " ASN A 166 " " NAG A1403 " - " ASN A 236 " " NAG A1404 " - " ASN A 244 " " NAG A1405 " - " ASN A 619 " " NAG A1406 " - " ASN A 774 " " NAG A1407 " - " ASN A 785 " " NAG A1408 " - " ASN A1176 " " NAG B1401 " - " ASN B1176 " " NAG B1402 " - " ASN B 619 " " NAG B1403 " - " ASN B 774 " " NAG B1404 " - " ASN B 236 " " NAG B1405 " - " ASN B 785 " " NAG B1406 " - " ASN B 166 " " NAG B1407 " - " ASN B 244 " " NAG B1408 " - " ASN B 104 " " NAG C1401 " - " ASN C 236 " " NAG C1402 " - " ASN C 104 " " NAG C1403 " - " ASN C1176 " " NAG C1404 " - " ASN C 166 " " NAG C1405 " - " ASN C 619 " " NAG C1406 " - " ASN C 785 " " NAG C1407 " - " ASN C 774 " " NAG C1408 " - " ASN C 244 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 222 " " NAG F 1 " - " ASN A 719 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN B 66 " " NAG J 1 " - " ASN B 719 " " NAG K 1 " - " ASN B 870 " " NAG L 1 " - " ASN B1213 " " NAG M 1 " - " ASN B 222 " " NAG N 1 " - " ASN C1213 " " NAG O 1 " - " ASN C 222 " " NAG P 1 " - " ASN C 870 " " NAG Q 1 " - " ASN C 66 " " NAG R 1 " - " ASN C 719 " Time building additional restraints: 8.32 Conformation dependent library (CDL) restraints added in 3.8 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 54 sheets defined 26.2% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.614A pdb=" N PHE A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.626A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.631A pdb=" N GLN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.842A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 removed outlier: 4.089A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.930A pdb=" N SER A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 4.066A pdb=" N MET A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 4.112A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 825 through 853 removed outlier: 4.271A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.837A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 959 removed outlier: 3.561A pdb=" N ALA A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 986 through 993 removed outlier: 3.676A pdb=" N LEU A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1008 removed outlier: 3.586A pdb=" N ILE A 997 " --> pdb=" O ASN A 993 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1039 removed outlier: 3.906A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 3.788A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.614A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.625A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 350 removed outlier: 3.630A pdb=" N GLN B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.842A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 removed outlier: 4.089A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 removed outlier: 3.929A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 4.066A pdb=" N MET B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 457 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 596 through 600 removed outlier: 4.113A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 825 through 853 removed outlier: 4.271A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.837A pdb=" N VAL B 929 " --> pdb=" O CYS B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 959 removed outlier: 3.561A pdb=" N ALA B 946 " --> pdb=" O ASN B 942 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 Processing helix chain 'B' and resid 986 through 993 removed outlier: 3.675A pdb=" N LEU B 990 " --> pdb=" O THR B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1008 removed outlier: 3.586A pdb=" N ILE B 997 " --> pdb=" O ASN B 993 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B1008 " --> pdb=" O ALA B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 3.905A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.788A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.614A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.625A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 350 removed outlier: 3.630A pdb=" N GLN C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.842A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 415 removed outlier: 4.089A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 3.930A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 4.065A pdb=" N MET C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 596 through 600 removed outlier: 4.112A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 825 through 853 removed outlier: 4.271A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 925 through 930 removed outlier: 3.838A pdb=" N VAL C 929 " --> pdb=" O CYS C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 959 removed outlier: 3.560A pdb=" N ALA C 946 " --> pdb=" O ASN C 942 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.676A pdb=" N LEU C 990 " --> pdb=" O THR C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1008 removed outlier: 3.585A pdb=" N ILE C 997 " --> pdb=" O ASN C 993 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1039 removed outlier: 3.905A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.788A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1198 through 1200 No H-bonds generated for 'chain 'C' and resid 1198 through 1200' Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.298A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 removed outlier: 4.093A pdb=" N SER A 88 " --> pdb=" O HIS A 298 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 300 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 284 removed outlier: 5.141A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 126 through 129 removed outlier: 4.286A pdb=" N SER A 126 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.129A pdb=" N TYR A 663 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.605A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.709A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.279A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 504 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 555 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 539 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 724 removed outlier: 6.949A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 732 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA A 737 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 795 removed outlier: 7.043A pdb=" N ASN A1145 " --> pdb=" O THR A 784 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 786 " --> pdb=" O PRO A1143 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE A 788 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A1141 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 790 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1139 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN A 792 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET A1137 " --> pdb=" O GLN A 792 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR A 794 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR A1135 " --> pdb=" O TYR A 794 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR A1135 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A1127 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET A1137 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER A1125 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A1139 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A1121 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 6.589A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1164 through 1167 removed outlier: 3.901A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1170 through 1173 Processing sheet with id=AC1, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.299A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AC3, first strand: chain 'B' and resid 88 through 89 removed outlier: 4.092A pdb=" N SER B 88 " --> pdb=" O HIS B 298 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 300 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.500A pdb=" N THR B 96 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AC6, first strand: chain 'B' and resid 280 through 284 removed outlier: 5.141A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 126 through 129 removed outlier: 4.285A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AC9, first strand: chain 'B' and resid 359 through 362 removed outlier: 4.129A pdb=" N TYR B 663 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.605A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.710A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.279A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 504 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 555 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 539 " --> pdb=" O GLY B 558 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 724 removed outlier: 6.950A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 732 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA B 737 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 778 through 795 removed outlier: 7.044A pdb=" N ASN B1145 " --> pdb=" O THR B 784 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 786 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE B 788 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B1141 " --> pdb=" O PHE B 788 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 790 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1139 " --> pdb=" O VAL B 790 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN B 792 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET B1137 " --> pdb=" O GLN B 792 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR B 794 " --> pdb=" O TYR B1135 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B1135 " --> pdb=" O TYR B 794 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR B1135 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL B1127 " --> pdb=" O TYR B1135 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET B1137 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B1125 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B1139 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B1121 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD7, first strand: chain 'B' and resid 1155 through 1157 removed outlier: 6.589A pdb=" N CYS B1156 " --> pdb=" O ILE B1214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1164 through 1167 removed outlier: 3.900A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1170 through 1173 Processing sheet with id=AE1, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.298A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AE3, first strand: chain 'C' and resid 88 through 89 removed outlier: 4.093A pdb=" N SER C 88 " --> pdb=" O HIS C 298 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 300 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE5, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AE6, first strand: chain 'C' and resid 280 through 284 removed outlier: 5.141A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 126 through 129 removed outlier: 4.286A pdb=" N SER C 126 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AE9, first strand: chain 'C' and resid 359 through 362 removed outlier: 4.129A pdb=" N TYR C 663 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR C 669 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 373 through 374 removed outlier: 6.605A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.709A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.280A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 504 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 555 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 539 " --> pdb=" O GLY C 558 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 724 removed outlier: 6.949A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 732 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA C 737 " --> pdb=" O PRO C 730 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 778 through 795 removed outlier: 7.043A pdb=" N ASN C1145 " --> pdb=" O THR C 784 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 786 " --> pdb=" O PRO C1143 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE C 788 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR C1141 " --> pdb=" O PHE C 788 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 790 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C1139 " --> pdb=" O VAL C 790 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN C 792 " --> pdb=" O MET C1137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET C1137 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR C 794 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR C1135 " --> pdb=" O TYR C 794 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR C1135 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL C1127 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET C1137 " --> pdb=" O SER C1125 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER C1125 " --> pdb=" O MET C1137 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C1139 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C1121 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF7, first strand: chain 'C' and resid 1155 through 1157 removed outlier: 6.588A pdb=" N CYS C1156 " --> pdb=" O ILE C1214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 1164 through 1167 removed outlier: 3.901A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1170 through 1173 977 hydrogen bonds defined for protein. 2574 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: 14.36 Time building geometry restraints manager: 9.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4785 1.32 - 1.45: 8076 1.45 - 1.58: 15477 1.58 - 1.70: 0 1.70 - 1.83: 204 Bond restraints: 28542 Sorted by residual: bond pdb=" CA GLU C 944 " pdb=" C GLU C 944 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.30e-02 5.92e+03 7.16e+01 bond pdb=" CA GLU B 944 " pdb=" C GLU B 944 " ideal model delta sigma weight residual 1.523 1.414 0.110 1.30e-02 5.92e+03 7.10e+01 bond pdb=" CA GLU A 944 " pdb=" C GLU A 944 " ideal model delta sigma weight residual 1.523 1.414 0.109 1.30e-02 5.92e+03 7.06e+01 bond pdb=" CA ASP A 940 " pdb=" C ASP A 940 " ideal model delta sigma weight residual 1.526 1.433 0.093 1.37e-02 5.33e+03 4.64e+01 bond pdb=" CA ASP C 940 " pdb=" C ASP C 940 " ideal model delta sigma weight residual 1.526 1.434 0.092 1.37e-02 5.33e+03 4.53e+01 ... (remaining 28537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 38170 2.70 - 5.40: 539 5.40 - 8.10: 102 8.10 - 10.80: 12 10.80 - 13.50: 6 Bond angle restraints: 38829 Sorted by residual: angle pdb=" N GLU A 944 " pdb=" CA GLU A 944 " pdb=" C GLU A 944 " ideal model delta sigma weight residual 111.28 97.78 13.50 1.09e+00 8.42e-01 1.53e+02 angle pdb=" N GLU C 944 " pdb=" CA GLU C 944 " pdb=" C GLU C 944 " ideal model delta sigma weight residual 111.28 97.80 13.48 1.09e+00 8.42e-01 1.53e+02 angle pdb=" N GLU B 944 " pdb=" CA GLU B 944 " pdb=" C GLU B 944 " ideal model delta sigma weight residual 111.28 97.83 13.45 1.09e+00 8.42e-01 1.52e+02 angle pdb=" CA ARG C 221 " pdb=" CB ARG C 221 " pdb=" CG ARG C 221 " ideal model delta sigma weight residual 114.10 124.28 -10.18 2.00e+00 2.50e-01 2.59e+01 angle pdb=" CA ARG B 221 " pdb=" CB ARG B 221 " pdb=" CG ARG B 221 " ideal model delta sigma weight residual 114.10 124.27 -10.17 2.00e+00 2.50e-01 2.58e+01 ... (remaining 38824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 16528 24.45 - 48.91: 935 48.91 - 73.36: 189 73.36 - 97.81: 99 97.81 - 122.26: 78 Dihedral angle restraints: 17829 sinusoidal: 7638 harmonic: 10191 Sorted by residual: dihedral pdb=" CB CYS A 811 " pdb=" SG CYS A 811 " pdb=" SG CYS A 817 " pdb=" CB CYS A 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.04 74.04 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.04 74.04 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS B 811 " pdb=" SG CYS B 811 " pdb=" SG CYS B 817 " pdb=" CB CYS B 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.02 74.02 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 17826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 4449 0.158 - 0.316: 72 0.316 - 0.474: 3 0.474 - 0.632: 0 0.632 - 0.790: 3 Chirality restraints: 4527 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 222 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 222 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 222 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.56e+01 ... (remaining 4524 not shown) Planarity restraints: 4989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 222 " 0.057 2.00e-02 2.50e+03 5.51e-02 3.79e+01 pdb=" CG ASN C 222 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN C 222 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 222 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 222 " 0.057 2.00e-02 2.50e+03 5.50e-02 3.79e+01 pdb=" CG ASN A 222 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 222 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 222 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 222 " -0.057 2.00e-02 2.50e+03 5.47e-02 3.74e+01 pdb=" CG ASN B 222 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN B 222 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 222 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.061 2.00e-02 2.50e+03 ... (remaining 4986 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3288 2.75 - 3.29: 26923 3.29 - 3.83: 47926 3.83 - 4.36: 52962 4.36 - 4.90: 90940 Nonbonded interactions: 222039 Sorted by model distance: nonbonded pdb=" OG SER A 268 " pdb=" O ASP A 272 " model vdw 2.218 3.040 nonbonded pdb=" OG SER C 268 " pdb=" O ASP C 272 " model vdw 2.218 3.040 nonbonded pdb=" OG SER B 268 " pdb=" O ASP B 272 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN C 421 " pdb=" OG1 THR C 483 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASN B 421 " pdb=" OG1 THR B 483 " model vdw 2.243 3.040 ... (remaining 222034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.120 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 72.080 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.220 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 28653 Z= 0.311 Angle : 0.922 23.640 39114 Z= 0.460 Chirality : 0.059 0.790 4527 Planarity : 0.006 0.091 4950 Dihedral : 18.729 122.263 11175 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 0.30 % Allowed : 0.56 % Favored : 99.14 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3462 helix: 0.29 (0.19), residues: 681 sheet: 0.42 (0.20), residues: 678 loop : -1.09 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1184 HIS 0.003 0.001 HIS A 836 PHE 0.026 0.002 PHE A 239 TYR 0.020 0.002 TYR A1141 ARG 0.011 0.001 ARG A 822 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 39) link_NAG-ASN : angle 6.71029 ( 117) link_ALPHA1-6 : bond 0.00670 ( 3) link_ALPHA1-6 : angle 1.44304 ( 9) link_BETA1-4 : bond 0.01171 ( 18) link_BETA1-4 : angle 4.38180 ( 54) hydrogen bonds : bond 0.13196 ( 977) hydrogen bonds : angle 7.13487 ( 2574) link_BETA1-6 : bond 0.01175 ( 3) link_BETA1-6 : angle 1.13852 ( 9) SS BOND : bond 0.00197 ( 48) SS BOND : angle 1.04644 ( 96) covalent geometry : bond 0.00528 (28542) covalent geometry : angle 0.83149 (38829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8948 (tmm) cc_final: 0.8482 (tmm) REVERT: A 576 GLN cc_start: 0.9089 (mp10) cc_final: 0.8827 (mp10) REVERT: A 938 LEU cc_start: 0.8098 (tp) cc_final: 0.7887 (tp) REVERT: B 84 MET cc_start: 0.8842 (tmm) cc_final: 0.8538 (tmm) REVERT: B 940 ASP cc_start: 0.6930 (m-30) cc_final: 0.6304 (m-30) REVERT: B 1053 ASP cc_start: 0.9039 (m-30) cc_final: 0.8412 (t70) REVERT: C 940 ASP cc_start: 0.7479 (m-30) cc_final: 0.7012 (m-30) outliers start: 9 outliers final: 2 residues processed: 241 average time/residue: 0.3425 time to fit residues: 140.8430 Evaluate side-chains 177 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 114 ASN A 226 ASN A 277 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 114 ASN B 226 ASN B 277 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 812 ASN B 842 GLN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 114 ASN C 226 ASN C 277 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN C 812 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.097954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.072935 restraints weight = 99917.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074730 restraints weight = 57578.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075941 restraints weight = 40836.708| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28653 Z= 0.240 Angle : 0.721 10.692 39114 Z= 0.351 Chirality : 0.047 0.371 4527 Planarity : 0.005 0.065 4950 Dihedral : 15.085 114.916 5085 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3462 helix: 0.78 (0.20), residues: 702 sheet: -0.04 (0.19), residues: 705 loop : -0.87 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 960 HIS 0.007 0.002 HIS C 264 PHE 0.016 0.002 PHE B 366 TYR 0.018 0.002 TYR A1211 ARG 0.003 0.001 ARG B 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 39) link_NAG-ASN : angle 3.91835 ( 117) link_ALPHA1-6 : bond 0.00317 ( 3) link_ALPHA1-6 : angle 1.91523 ( 9) link_BETA1-4 : bond 0.00686 ( 18) link_BETA1-4 : angle 3.10952 ( 54) hydrogen bonds : bond 0.04244 ( 977) hydrogen bonds : angle 5.80583 ( 2574) link_BETA1-6 : bond 0.01429 ( 3) link_BETA1-6 : angle 1.66154 ( 9) SS BOND : bond 0.00307 ( 48) SS BOND : angle 0.97615 ( 96) covalent geometry : bond 0.00525 (28542) covalent geometry : angle 0.67797 (38829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7458 (t-90) cc_final: 0.6243 (t-90) REVERT: A 213 ASP cc_start: 0.8041 (m-30) cc_final: 0.6970 (t70) REVERT: A 240 MET cc_start: 0.8315 (tpp) cc_final: 0.7858 (tpt) REVERT: A 580 ASP cc_start: 0.7524 (t0) cc_final: 0.7205 (t0) REVERT: A 757 MET cc_start: 0.8379 (mpp) cc_final: 0.7875 (mpp) REVERT: A 940 ASP cc_start: 0.6495 (m-30) cc_final: 0.5131 (m-30) REVERT: A 1008 MET cc_start: 0.7498 (ppp) cc_final: 0.6731 (ppp) REVERT: B 240 MET cc_start: 0.8349 (tpp) cc_final: 0.7972 (tpp) REVERT: B 326 ASP cc_start: 0.8149 (t0) cc_final: 0.7945 (t0) REVERT: B 940 ASP cc_start: 0.6798 (m-30) cc_final: 0.5602 (m-30) REVERT: B 1008 MET cc_start: 0.7619 (ppp) cc_final: 0.7076 (ppp) REVERT: B 1053 ASP cc_start: 0.9195 (m-30) cc_final: 0.8827 (t70) REVERT: C 208 HIS cc_start: 0.6786 (t-90) cc_final: 0.5166 (t-90) REVERT: C 213 ASP cc_start: 0.7790 (m-30) cc_final: 0.6924 (t70) REVERT: C 731 LEU cc_start: 0.8641 (tp) cc_final: 0.8375 (tp) REVERT: C 940 ASP cc_start: 0.6702 (m-30) cc_final: 0.5821 (m-30) REVERT: C 1053 ASP cc_start: 0.9068 (m-30) cc_final: 0.8614 (t70) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3689 time to fit residues: 135.9660 Evaluate side-chains 167 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 319 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 345 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074609 restraints weight = 98415.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076526 restraints weight = 56444.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077794 restraints weight = 39424.738| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28653 Z= 0.135 Angle : 0.624 10.886 39114 Z= 0.299 Chirality : 0.045 0.308 4527 Planarity : 0.005 0.062 4950 Dihedral : 14.280 117.949 5085 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3462 helix: 1.10 (0.21), residues: 708 sheet: -0.04 (0.19), residues: 714 loop : -0.81 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 253 HIS 0.003 0.001 HIS A 836 PHE 0.017 0.001 PHE A 366 TYR 0.019 0.001 TYR B1141 ARG 0.003 0.000 ARG A 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 39) link_NAG-ASN : angle 3.51329 ( 117) link_ALPHA1-6 : bond 0.01025 ( 3) link_ALPHA1-6 : angle 1.45988 ( 9) link_BETA1-4 : bond 0.00323 ( 18) link_BETA1-4 : angle 2.68909 ( 54) hydrogen bonds : bond 0.03697 ( 977) hydrogen bonds : angle 5.50423 ( 2574) link_BETA1-6 : bond 0.01694 ( 3) link_BETA1-6 : angle 1.67342 ( 9) SS BOND : bond 0.00292 ( 48) SS BOND : angle 0.81299 ( 96) covalent geometry : bond 0.00296 (28542) covalent geometry : angle 0.58517 (38829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9023 (tmm) cc_final: 0.8644 (tmm) REVERT: A 208 HIS cc_start: 0.7322 (t-90) cc_final: 0.6082 (t-90) REVERT: A 213 ASP cc_start: 0.8096 (m-30) cc_final: 0.6998 (t70) REVERT: A 292 TYR cc_start: 0.8300 (m-80) cc_final: 0.7976 (m-80) REVERT: A 580 ASP cc_start: 0.7644 (t0) cc_final: 0.7336 (t0) REVERT: A 940 ASP cc_start: 0.6332 (m-30) cc_final: 0.5490 (m-30) REVERT: A 1053 ASP cc_start: 0.9168 (m-30) cc_final: 0.8736 (t70) REVERT: B 208 HIS cc_start: 0.7261 (t-90) cc_final: 0.6148 (t-90) REVERT: B 213 ASP cc_start: 0.7957 (m-30) cc_final: 0.7187 (t70) REVERT: B 326 ASP cc_start: 0.8222 (t0) cc_final: 0.8002 (t0) REVERT: B 940 ASP cc_start: 0.6672 (m-30) cc_final: 0.5576 (m-30) REVERT: B 1008 MET cc_start: 0.7280 (ppp) cc_final: 0.6989 (ppp) REVERT: B 1053 ASP cc_start: 0.9150 (m-30) cc_final: 0.8740 (t70) REVERT: B 1189 SER cc_start: 0.9109 (m) cc_final: 0.8751 (p) REVERT: C 105 TYR cc_start: 0.8744 (m-80) cc_final: 0.8460 (m-80) REVERT: C 326 ASP cc_start: 0.8219 (t0) cc_final: 0.8003 (t0) REVERT: C 731 LEU cc_start: 0.8576 (tp) cc_final: 0.8270 (tp) REVERT: C 939 MET cc_start: 0.7326 (mmm) cc_final: 0.6974 (mmm) REVERT: C 940 ASP cc_start: 0.6872 (m-30) cc_final: 0.5790 (m-30) REVERT: C 1053 ASP cc_start: 0.9025 (m-30) cc_final: 0.8605 (t70) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3306 time to fit residues: 127.3084 Evaluate side-chains 171 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 7 optimal weight: 20.0000 chunk 319 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 273 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 chunk 257 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 164 optimal weight: 30.0000 chunk 140 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 280 GLN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 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 = 0.3761 r_free = 0.3761 target = 0.098303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073041 restraints weight = 99744.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074878 restraints weight = 56476.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.076117 restraints weight = 39579.792| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28653 Z= 0.149 Angle : 0.625 11.101 39114 Z= 0.299 Chirality : 0.044 0.245 4527 Planarity : 0.004 0.060 4950 Dihedral : 13.577 118.396 5085 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3462 helix: 1.21 (0.21), residues: 708 sheet: -0.14 (0.19), residues: 681 loop : -0.82 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 253 HIS 0.003 0.001 HIS B 264 PHE 0.015 0.001 PHE A 366 TYR 0.014 0.001 TYR B 794 ARG 0.002 0.000 ARG A 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 39) link_NAG-ASN : angle 3.29181 ( 117) link_ALPHA1-6 : bond 0.00958 ( 3) link_ALPHA1-6 : angle 1.46014 ( 9) link_BETA1-4 : bond 0.00365 ( 18) link_BETA1-4 : angle 2.57303 ( 54) hydrogen bonds : bond 0.03573 ( 977) hydrogen bonds : angle 5.36404 ( 2574) link_BETA1-6 : bond 0.01740 ( 3) link_BETA1-6 : angle 1.75485 ( 9) SS BOND : bond 0.00261 ( 48) SS BOND : angle 1.08159 ( 96) covalent geometry : bond 0.00333 (28542) covalent geometry : angle 0.58928 (38829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8998 (tmm) cc_final: 0.8585 (tmm) REVERT: A 208 HIS cc_start: 0.7240 (t-90) cc_final: 0.5958 (t-90) REVERT: A 213 ASP cc_start: 0.8127 (m-30) cc_final: 0.6936 (t70) REVERT: A 240 MET cc_start: 0.8420 (tpt) cc_final: 0.8203 (tpp) REVERT: A 292 TYR cc_start: 0.8408 (m-80) cc_final: 0.8034 (m-80) REVERT: A 580 ASP cc_start: 0.7674 (t0) cc_final: 0.7420 (t0) REVERT: A 757 MET cc_start: 0.8381 (mpp) cc_final: 0.7612 (mpp) REVERT: A 940 ASP cc_start: 0.6600 (m-30) cc_final: 0.5622 (m-30) REVERT: A 1053 ASP cc_start: 0.9199 (m-30) cc_final: 0.8754 (t70) REVERT: B 84 MET cc_start: 0.8869 (tmm) cc_final: 0.8481 (tmm) REVERT: B 105 TYR cc_start: 0.8744 (m-80) cc_final: 0.8442 (m-80) REVERT: B 208 HIS cc_start: 0.7267 (t-90) cc_final: 0.6067 (t-90) REVERT: B 213 ASP cc_start: 0.7993 (m-30) cc_final: 0.7143 (t70) REVERT: B 240 MET cc_start: 0.8064 (tpt) cc_final: 0.7744 (tpp) REVERT: B 940 ASP cc_start: 0.6692 (m-30) cc_final: 0.5589 (m-30) REVERT: B 943 MET cc_start: 0.8352 (tpt) cc_final: 0.8127 (tpt) REVERT: B 1008 MET cc_start: 0.7294 (ppp) cc_final: 0.7073 (ppp) REVERT: B 1053 ASP cc_start: 0.9178 (m-30) cc_final: 0.8744 (t70) REVERT: B 1189 SER cc_start: 0.9075 (m) cc_final: 0.8748 (p) REVERT: C 105 TYR cc_start: 0.8729 (m-80) cc_final: 0.8473 (m-80) REVERT: C 326 ASP cc_start: 0.8244 (t0) cc_final: 0.8039 (t0) REVERT: C 794 TYR cc_start: 0.8834 (t80) cc_final: 0.8621 (t80) REVERT: C 940 ASP cc_start: 0.6558 (m-30) cc_final: 0.5914 (m-30) REVERT: C 1053 ASP cc_start: 0.9056 (m-30) cc_final: 0.8627 (t70) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3616 time to fit residues: 139.0663 Evaluate side-chains 174 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 287 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 334 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A 842 GLN B 114 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN C 772 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.097070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071618 restraints weight = 99505.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073467 restraints weight = 56862.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074674 restraints weight = 40056.927| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28653 Z= 0.179 Angle : 0.653 11.357 39114 Z= 0.315 Chirality : 0.045 0.236 4527 Planarity : 0.004 0.062 4950 Dihedral : 13.258 119.366 5085 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3462 helix: 1.27 (0.21), residues: 690 sheet: -0.16 (0.18), residues: 798 loop : -0.85 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 44 HIS 0.004 0.001 HIS A 264 PHE 0.017 0.001 PHE B 778 TYR 0.019 0.001 TYR B1153 ARG 0.002 0.000 ARG A 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 39) link_NAG-ASN : angle 3.33171 ( 117) link_ALPHA1-6 : bond 0.00686 ( 3) link_ALPHA1-6 : angle 1.47536 ( 9) link_BETA1-4 : bond 0.00314 ( 18) link_BETA1-4 : angle 2.48113 ( 54) hydrogen bonds : bond 0.03704 ( 977) hydrogen bonds : angle 5.42049 ( 2574) link_BETA1-6 : bond 0.01819 ( 3) link_BETA1-6 : angle 1.91134 ( 9) SS BOND : bond 0.00319 ( 48) SS BOND : angle 1.12481 ( 96) covalent geometry : bond 0.00400 (28542) covalent geometry : angle 0.61940 (38829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7251 (t-90) cc_final: 0.5834 (t-90) REVERT: A 213 ASP cc_start: 0.8186 (m-30) cc_final: 0.6971 (t70) REVERT: A 240 MET cc_start: 0.8385 (tpt) cc_final: 0.7775 (tpt) REVERT: A 292 TYR cc_start: 0.8410 (m-80) cc_final: 0.8031 (m-80) REVERT: A 580 ASP cc_start: 0.7802 (t0) cc_final: 0.7551 (t0) REVERT: A 757 MET cc_start: 0.8449 (mpp) cc_final: 0.7710 (mpp) REVERT: A 940 ASP cc_start: 0.6923 (m-30) cc_final: 0.5886 (m-30) REVERT: A 1008 MET cc_start: 0.7439 (ppp) cc_final: 0.6393 (ppp) REVERT: A 1053 ASP cc_start: 0.9187 (m-30) cc_final: 0.8750 (t70) REVERT: B 105 TYR cc_start: 0.8811 (m-80) cc_final: 0.8523 (m-80) REVERT: B 240 MET cc_start: 0.8224 (tpt) cc_final: 0.7955 (tpp) REVERT: B 326 ASP cc_start: 0.8291 (t0) cc_final: 0.8015 (t0) REVERT: B 940 ASP cc_start: 0.6980 (m-30) cc_final: 0.5764 (m-30) REVERT: B 943 MET cc_start: 0.8343 (tpt) cc_final: 0.8112 (tpt) REVERT: B 1053 ASP cc_start: 0.9170 (m-30) cc_final: 0.8736 (t70) REVERT: B 1189 SER cc_start: 0.9151 (m) cc_final: 0.8800 (p) REVERT: C 208 HIS cc_start: 0.7139 (t-90) cc_final: 0.6175 (t-170) REVERT: C 213 ASP cc_start: 0.7764 (m-30) cc_final: 0.6854 (t70) REVERT: C 731 LEU cc_start: 0.8706 (tp) cc_final: 0.8414 (tp) REVERT: C 1053 ASP cc_start: 0.9094 (m-30) cc_final: 0.8631 (t70) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3258 time to fit residues: 134.1289 Evaluate side-chains 169 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 237 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 338 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 149 optimal weight: 0.0980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN B 208 HIS B 280 GLN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 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 = 0.3744 r_free = 0.3744 target = 0.097319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.071904 restraints weight = 99684.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073764 restraints weight = 56719.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.075033 restraints weight = 39674.912| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28653 Z= 0.164 Angle : 0.648 11.693 39114 Z= 0.311 Chirality : 0.044 0.234 4527 Planarity : 0.004 0.060 4950 Dihedral : 12.903 119.834 5085 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3462 helix: 1.40 (0.21), residues: 681 sheet: -0.25 (0.17), residues: 798 loop : -0.88 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 253 HIS 0.003 0.001 HIS A 836 PHE 0.032 0.001 PHE B 164 TYR 0.019 0.001 TYR A1153 ARG 0.002 0.000 ARG C 887 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 39) link_NAG-ASN : angle 3.24273 ( 117) link_ALPHA1-6 : bond 0.00605 ( 3) link_ALPHA1-6 : angle 1.43829 ( 9) link_BETA1-4 : bond 0.00275 ( 18) link_BETA1-4 : angle 2.42160 ( 54) hydrogen bonds : bond 0.03680 ( 977) hydrogen bonds : angle 5.35286 ( 2574) link_BETA1-6 : bond 0.01715 ( 3) link_BETA1-6 : angle 1.98337 ( 9) SS BOND : bond 0.00199 ( 48) SS BOND : angle 1.14220 ( 96) covalent geometry : bond 0.00367 (28542) covalent geometry : angle 0.61517 (38829) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8957 (tmm) cc_final: 0.8590 (tmm) REVERT: A 208 HIS cc_start: 0.7377 (t-90) cc_final: 0.6446 (t-170) REVERT: A 213 ASP cc_start: 0.8151 (m-30) cc_final: 0.6814 (t70) REVERT: A 240 MET cc_start: 0.8381 (tpt) cc_final: 0.7928 (tpt) REVERT: A 241 TYR cc_start: 0.8733 (m-10) cc_final: 0.8498 (m-10) REVERT: A 580 ASP cc_start: 0.7809 (t0) cc_final: 0.7570 (t0) REVERT: A 757 MET cc_start: 0.8448 (mpp) cc_final: 0.7689 (mpp) REVERT: A 1053 ASP cc_start: 0.9179 (m-30) cc_final: 0.8744 (t70) REVERT: B 84 MET cc_start: 0.8887 (tmm) cc_final: 0.8558 (tmm) REVERT: B 105 TYR cc_start: 0.8834 (m-80) cc_final: 0.8527 (m-10) REVERT: B 208 HIS cc_start: 0.7008 (t70) cc_final: 0.6686 (t-170) REVERT: B 213 ASP cc_start: 0.7803 (m-30) cc_final: 0.7104 (t70) REVERT: B 240 MET cc_start: 0.8297 (tpt) cc_final: 0.8061 (tpp) REVERT: B 326 ASP cc_start: 0.8290 (t0) cc_final: 0.8019 (t0) REVERT: B 940 ASP cc_start: 0.7073 (m-30) cc_final: 0.5888 (m-30) REVERT: B 1053 ASP cc_start: 0.9172 (m-30) cc_final: 0.8748 (t70) REVERT: B 1189 SER cc_start: 0.9092 (m) cc_final: 0.8782 (p) REVERT: C 105 TYR cc_start: 0.8761 (m-80) cc_final: 0.8508 (m-10) REVERT: C 326 ASP cc_start: 0.8331 (t0) cc_final: 0.8022 (t0) REVERT: C 731 LEU cc_start: 0.8741 (tp) cc_final: 0.8464 (tp) REVERT: C 1053 ASP cc_start: 0.9078 (m-30) cc_final: 0.8627 (t70) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3283 time to fit residues: 132.3897 Evaluate side-chains 172 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 314 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN C 208 HIS ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 GLN ** C 857 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 = 0.3711 r_free = 0.3711 target = 0.095694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070400 restraints weight = 99955.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072184 restraints weight = 57211.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.073347 restraints weight = 40382.570| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28653 Z= 0.219 Angle : 0.709 14.314 39114 Z= 0.344 Chirality : 0.046 0.222 4527 Planarity : 0.005 0.061 4950 Dihedral : 12.747 120.083 5085 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3462 helix: 0.98 (0.20), residues: 702 sheet: -0.83 (0.17), residues: 798 loop : -0.89 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 960 HIS 0.005 0.001 HIS B 264 PHE 0.032 0.002 PHE B 164 TYR 0.021 0.002 TYR B 794 ARG 0.005 0.001 ARG A 979 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 39) link_NAG-ASN : angle 3.38056 ( 117) link_ALPHA1-6 : bond 0.00424 ( 3) link_ALPHA1-6 : angle 1.49520 ( 9) link_BETA1-4 : bond 0.00292 ( 18) link_BETA1-4 : angle 2.46374 ( 54) hydrogen bonds : bond 0.03989 ( 977) hydrogen bonds : angle 5.57010 ( 2574) link_BETA1-6 : bond 0.01803 ( 3) link_BETA1-6 : angle 2.14596 ( 9) SS BOND : bond 0.00302 ( 48) SS BOND : angle 1.15594 ( 96) covalent geometry : bond 0.00485 (28542) covalent geometry : angle 0.67756 (38829) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8995 (tmm) cc_final: 0.8632 (tmm) REVERT: A 240 MET cc_start: 0.8342 (tpt) cc_final: 0.8024 (tpt) REVERT: A 241 TYR cc_start: 0.8817 (m-10) cc_final: 0.8611 (m-10) REVERT: A 326 ASP cc_start: 0.8305 (t0) cc_final: 0.8069 (t0) REVERT: A 1008 MET cc_start: 0.7561 (ppp) cc_final: 0.6463 (ppp) REVERT: A 1053 ASP cc_start: 0.9185 (m-30) cc_final: 0.8734 (t70) REVERT: B 84 MET cc_start: 0.8943 (tmm) cc_final: 0.8654 (tmm) REVERT: B 208 HIS cc_start: 0.7566 (t70) cc_final: 0.6280 (t70) REVERT: B 213 ASP cc_start: 0.8112 (m-30) cc_final: 0.7063 (t70) REVERT: B 326 ASP cc_start: 0.8297 (t0) cc_final: 0.8075 (t0) REVERT: B 1053 ASP cc_start: 0.9189 (m-30) cc_final: 0.8771 (t70) REVERT: B 1148 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7950 (mm-30) REVERT: C 208 HIS cc_start: 0.7487 (t70) cc_final: 0.6493 (t-170) REVERT: C 213 ASP cc_start: 0.7640 (m-30) cc_final: 0.6756 (t70) REVERT: C 326 ASP cc_start: 0.8285 (t0) cc_final: 0.8031 (t0) REVERT: C 1053 ASP cc_start: 0.9061 (m-30) cc_final: 0.8679 (t70) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3237 time to fit residues: 125.0709 Evaluate side-chains 165 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 215 optimal weight: 0.0570 chunk 279 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 335 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.095777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.071067 restraints weight = 100441.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072852 restraints weight = 57780.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074039 restraints weight = 40836.502| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28653 Z= 0.233 Angle : 0.722 11.596 39114 Z= 0.351 Chirality : 0.046 0.229 4527 Planarity : 0.005 0.062 4950 Dihedral : 12.551 120.330 5085 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3462 helix: 0.86 (0.20), residues: 702 sheet: -0.75 (0.18), residues: 768 loop : -0.99 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 44 HIS 0.006 0.001 HIS C 264 PHE 0.025 0.002 PHE B 164 TYR 0.031 0.002 TYR C 105 ARG 0.004 0.001 ARG A 887 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 39) link_NAG-ASN : angle 3.42778 ( 117) link_ALPHA1-6 : bond 0.00315 ( 3) link_ALPHA1-6 : angle 1.51222 ( 9) link_BETA1-4 : bond 0.00303 ( 18) link_BETA1-4 : angle 2.51761 ( 54) hydrogen bonds : bond 0.04005 ( 977) hydrogen bonds : angle 5.63180 ( 2574) link_BETA1-6 : bond 0.01654 ( 3) link_BETA1-6 : angle 2.27855 ( 9) SS BOND : bond 0.00246 ( 48) SS BOND : angle 1.36935 ( 96) covalent geometry : bond 0.00518 (28542) covalent geometry : angle 0.68877 (38829) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9041 (tmm) cc_final: 0.8691 (tmm) REVERT: A 208 HIS cc_start: 0.7528 (t-90) cc_final: 0.6641 (t-170) REVERT: A 213 ASP cc_start: 0.7989 (m-30) cc_final: 0.6718 (t70) REVERT: A 240 MET cc_start: 0.8197 (tpt) cc_final: 0.7977 (tpt) REVERT: A 241 TYR cc_start: 0.8863 (m-10) cc_final: 0.8560 (m-10) REVERT: A 326 ASP cc_start: 0.8352 (t0) cc_final: 0.8083 (t0) REVERT: A 757 MET cc_start: 0.8320 (mpp) cc_final: 0.7568 (mpp) REVERT: A 1008 MET cc_start: 0.7564 (ppp) cc_final: 0.6468 (ppp) REVERT: A 1053 ASP cc_start: 0.9136 (m-30) cc_final: 0.8724 (t70) REVERT: B 84 MET cc_start: 0.8952 (tmm) cc_final: 0.8703 (tmm) REVERT: B 208 HIS cc_start: 0.7745 (t70) cc_final: 0.6481 (t70) REVERT: B 213 ASP cc_start: 0.8062 (m-30) cc_final: 0.6943 (t70) REVERT: B 326 ASP cc_start: 0.8373 (t0) cc_final: 0.8142 (t0) REVERT: B 1053 ASP cc_start: 0.9155 (m-30) cc_final: 0.8726 (t70) REVERT: C 148 MET cc_start: 0.7496 (tmm) cc_final: 0.7275 (tmm) REVERT: C 208 HIS cc_start: 0.7772 (t70) cc_final: 0.6555 (t-170) REVERT: C 213 ASP cc_start: 0.7925 (m-30) cc_final: 0.6906 (t70) REVERT: C 326 ASP cc_start: 0.8336 (t0) cc_final: 0.8025 (t0) REVERT: C 1053 ASP cc_start: 0.9032 (m-30) cc_final: 0.8628 (t70) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3363 time to fit residues: 123.6057 Evaluate side-chains 166 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 303 optimal weight: 10.0000 chunk 345 optimal weight: 1.9990 chunk 314 optimal weight: 0.8980 chunk 342 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 232 optimal weight: 50.0000 chunk 257 optimal weight: 7.9990 chunk 116 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.097322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072753 restraints weight = 99403.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074584 restraints weight = 56333.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.075811 restraints weight = 39559.889| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28653 Z= 0.152 Angle : 0.668 12.283 39114 Z= 0.320 Chirality : 0.045 0.221 4527 Planarity : 0.004 0.062 4950 Dihedral : 12.000 120.607 5085 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3462 helix: 0.91 (0.20), residues: 720 sheet: -0.67 (0.18), residues: 762 loop : -0.94 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.003 0.001 HIS A 836 PHE 0.027 0.001 PHE B 239 TYR 0.029 0.001 TYR B 105 ARG 0.003 0.000 ARG B 887 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 39) link_NAG-ASN : angle 3.22933 ( 117) link_ALPHA1-6 : bond 0.00408 ( 3) link_ALPHA1-6 : angle 1.41039 ( 9) link_BETA1-4 : bond 0.00239 ( 18) link_BETA1-4 : angle 2.57724 ( 54) hydrogen bonds : bond 0.03641 ( 977) hydrogen bonds : angle 5.43604 ( 2574) link_BETA1-6 : bond 0.01605 ( 3) link_BETA1-6 : angle 2.41009 ( 9) SS BOND : bond 0.00209 ( 48) SS BOND : angle 1.25877 ( 96) covalent geometry : bond 0.00343 (28542) covalent geometry : angle 0.63542 (38829) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9069 (tmm) cc_final: 0.8732 (tmm) REVERT: A 208 HIS cc_start: 0.7450 (t-90) cc_final: 0.6500 (t-170) REVERT: A 213 ASP cc_start: 0.8013 (m-30) cc_final: 0.6767 (t70) REVERT: A 326 ASP cc_start: 0.8363 (t0) cc_final: 0.8115 (t0) REVERT: A 757 MET cc_start: 0.8281 (mpp) cc_final: 0.7495 (mpp) REVERT: A 1008 MET cc_start: 0.7445 (ppp) cc_final: 0.6371 (ppp) REVERT: A 1053 ASP cc_start: 0.9121 (m-30) cc_final: 0.8707 (t70) REVERT: B 326 ASP cc_start: 0.8224 (t0) cc_final: 0.7979 (t0) REVERT: B 1053 ASP cc_start: 0.9132 (m-30) cc_final: 0.8701 (t70) REVERT: C 208 HIS cc_start: 0.7590 (t70) cc_final: 0.6165 (t-170) REVERT: C 213 ASP cc_start: 0.7820 (m-30) cc_final: 0.6779 (t70) REVERT: C 326 ASP cc_start: 0.8260 (t0) cc_final: 0.8008 (t0) REVERT: C 725 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6822 (tt0) REVERT: C 777 TYR cc_start: 0.8088 (m-10) cc_final: 0.7807 (m-80) REVERT: C 1053 ASP cc_start: 0.9019 (m-30) cc_final: 0.8625 (t70) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3345 time to fit residues: 132.9623 Evaluate side-chains 162 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 226 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 330 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 332 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.096450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.071843 restraints weight = 99417.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073630 restraints weight = 56787.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074828 restraints weight = 40106.501| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28653 Z= 0.186 Angle : 0.686 11.760 39114 Z= 0.331 Chirality : 0.045 0.252 4527 Planarity : 0.005 0.061 4950 Dihedral : 11.721 120.531 5085 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3462 helix: 0.85 (0.20), residues: 720 sheet: -0.64 (0.18), residues: 750 loop : -1.02 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 836 PHE 0.032 0.002 PHE C 239 TYR 0.027 0.002 TYR B 105 ARG 0.002 0.000 ARG A 887 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 39) link_NAG-ASN : angle 3.23758 ( 117) link_ALPHA1-6 : bond 0.00305 ( 3) link_ALPHA1-6 : angle 1.49192 ( 9) link_BETA1-4 : bond 0.00248 ( 18) link_BETA1-4 : angle 2.65908 ( 54) hydrogen bonds : bond 0.03749 ( 977) hydrogen bonds : angle 5.46628 ( 2574) link_BETA1-6 : bond 0.01686 ( 3) link_BETA1-6 : angle 2.60030 ( 9) SS BOND : bond 0.00232 ( 48) SS BOND : angle 1.20370 ( 96) covalent geometry : bond 0.00417 (28542) covalent geometry : angle 0.65322 (38829) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9170 (tmm) cc_final: 0.8867 (tmm) REVERT: A 208 HIS cc_start: 0.7473 (t-90) cc_final: 0.6361 (t-170) REVERT: A 213 ASP cc_start: 0.7966 (m-30) cc_final: 0.6844 (t70) REVERT: A 326 ASP cc_start: 0.8363 (t0) cc_final: 0.8116 (t0) REVERT: A 757 MET cc_start: 0.8317 (mpp) cc_final: 0.7566 (mpp) REVERT: A 1008 MET cc_start: 0.7491 (ppp) cc_final: 0.6419 (ppp) REVERT: A 1053 ASP cc_start: 0.9105 (m-30) cc_final: 0.8671 (t70) REVERT: B 326 ASP cc_start: 0.8283 (t0) cc_final: 0.8052 (t0) REVERT: B 1053 ASP cc_start: 0.9146 (m-30) cc_final: 0.8626 (t70) REVERT: C 326 ASP cc_start: 0.8270 (t0) cc_final: 0.8004 (t0) REVERT: C 777 TYR cc_start: 0.8177 (m-10) cc_final: 0.7915 (m-80) REVERT: C 1053 ASP cc_start: 0.9026 (m-30) cc_final: 0.8602 (t70) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3429 time to fit residues: 130.4795 Evaluate side-chains 158 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 159 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 334 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 137 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** 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 = 0.3752 r_free = 0.3752 target = 0.097495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072948 restraints weight = 99354.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074829 restraints weight = 56497.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076061 restraints weight = 39577.930| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28653 Z= 0.149 Angle : 0.668 12.117 39114 Z= 0.321 Chirality : 0.045 0.223 4527 Planarity : 0.004 0.062 4950 Dihedral : 11.233 120.065 5085 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3462 helix: 0.89 (0.20), residues: 726 sheet: -0.71 (0.18), residues: 768 loop : -0.88 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 253 HIS 0.003 0.001 HIS A 836 PHE 0.029 0.001 PHE C 164 TYR 0.025 0.001 TYR B 105 ARG 0.003 0.000 ARG C 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 39) link_NAG-ASN : angle 3.12704 ( 117) link_ALPHA1-6 : bond 0.00354 ( 3) link_ALPHA1-6 : angle 1.43506 ( 9) link_BETA1-4 : bond 0.00234 ( 18) link_BETA1-4 : angle 2.72514 ( 54) hydrogen bonds : bond 0.03590 ( 977) hydrogen bonds : angle 5.37654 ( 2574) link_BETA1-6 : bond 0.01860 ( 3) link_BETA1-6 : angle 2.72304 ( 9) SS BOND : bond 0.00206 ( 48) SS BOND : angle 1.12899 ( 96) covalent geometry : bond 0.00335 (28542) covalent geometry : angle 0.63609 (38829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8415.56 seconds wall clock time: 147 minutes 57.28 seconds (8877.28 seconds total)