Starting phenix.real_space_refine on Mon Aug 25 13:05:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yn0_33949/08_2025/7yn0_33949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yn0_33949/08_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_33949/08_2025/7yn0_33949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yn0_33949/08_2025/7yn0_33949.map" model { file = "/net/cci-nas-00/data/ceres_data/7yn0_33949/08_2025/7yn0_33949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yn0_33949/08_2025/7yn0_33949.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.10, per 1000 atoms: 0.25 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: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.49 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: 7.83 Time building geometry restraints manager: 3.49 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: 0.08 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: 1.100 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.280 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- 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 : 5.70 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (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 ARG 0.011 0.001 ARG A 822 TYR 0.020 0.002 TYR A1141 PHE 0.026 0.002 PHE A 239 TRP 0.007 0.001 TRP B1184 HIS 0.003 0.001 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.00528 (28542) covalent geometry : angle 0.83149 (38829) SS BOND : bond 0.00197 ( 48) SS BOND : angle 1.04644 ( 96) hydrogen bonds : bond 0.13196 ( 977) hydrogen bonds : angle 7.13487 ( 2574) 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) link_BETA1-6 : bond 0.01175 ( 3) link_BETA1-6 : angle 1.13852 ( 9) link_NAG-ASN : bond 0.00504 ( 39) link_NAG-ASN : angle 6.71029 ( 117) *********************** 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 : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8948 (tmm) cc_final: 0.8481 (tmm) REVERT: A 576 GLN cc_start: 0.9089 (mp10) cc_final: 0.8828 (mp10) REVERT: A 938 LEU cc_start: 0.8098 (tp) cc_final: 0.7888 (tp) REVERT: B 84 MET cc_start: 0.8842 (tmm) cc_final: 0.8539 (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: 0.8413 (t70) REVERT: C 940 ASP cc_start: 0.7479 (m-30) cc_final: 0.7011 (m-30) outliers start: 9 outliers final: 2 residues processed: 241 average time/residue: 0.1709 time to fit residues: 70.3129 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 : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 277 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 842 GLN ** 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 519 ASN C 812 ASN C 842 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.096837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.071704 restraints weight = 100072.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073452 restraints weight = 57859.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074581 restraints weight = 41232.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075341 restraints weight = 33492.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.075733 restraints weight = 29345.764| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28653 Z= 0.288 Angle : 0.775 10.887 39114 Z= 0.381 Chirality : 0.049 0.345 4527 Planarity : 0.005 0.063 4950 Dihedral : 14.958 114.931 5085 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.14), residues: 3462 helix: 0.76 (0.20), residues: 699 sheet: -0.22 (0.19), residues: 705 loop : -0.97 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 979 TYR 0.022 0.002 TYR A1211 PHE 0.019 0.002 PHE B 366 TRP 0.008 0.001 TRP A 960 HIS 0.008 0.002 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00628 (28542) covalent geometry : angle 0.73484 (38829) SS BOND : bond 0.00354 ( 48) SS BOND : angle 1.09850 ( 96) hydrogen bonds : bond 0.04414 ( 977) hydrogen bonds : angle 5.89493 ( 2574) link_ALPHA1-6 : bond 0.00637 ( 3) link_ALPHA1-6 : angle 1.71208 ( 9) link_BETA1-4 : bond 0.00755 ( 18) link_BETA1-4 : angle 3.19869 ( 54) link_BETA1-6 : bond 0.02672 ( 3) link_BETA1-6 : angle 1.98944 ( 9) link_NAG-ASN : bond 0.00452 ( 39) link_NAG-ASN : angle 3.92182 ( 117) *********************** 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 216 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7460 (t-90) cc_final: 0.6276 (t-90) REVERT: A 213 ASP cc_start: 0.8030 (m-30) cc_final: 0.6946 (t70) REVERT: A 580 ASP cc_start: 0.7677 (t0) cc_final: 0.7384 (t0) REVERT: A 757 MET cc_start: 0.8420 (mpp) cc_final: 0.8002 (mpp) REVERT: A 1008 MET cc_start: 0.7507 (ppp) cc_final: 0.6737 (ppp) REVERT: B 105 TYR cc_start: 0.8621 (m-80) cc_final: 0.8213 (m-80) REVERT: B 208 HIS cc_start: 0.7093 (t-90) cc_final: 0.5483 (t-90) REVERT: B 213 ASP cc_start: 0.8090 (m-30) cc_final: 0.7088 (t70) REVERT: B 240 MET cc_start: 0.8321 (tpp) cc_final: 0.7985 (tpp) REVERT: B 940 ASP cc_start: 0.6858 (m-30) cc_final: 0.5752 (m-30) REVERT: B 1008 MET cc_start: 0.7617 (ppp) cc_final: 0.7114 (ppp) REVERT: B 1053 ASP cc_start: 0.9162 (m-30) cc_final: 0.8787 (t70) REVERT: C 105 TYR cc_start: 0.8636 (m-80) cc_final: 0.8324 (m-80) REVERT: C 208 HIS cc_start: 0.6895 (t-90) cc_final: 0.5253 (t-90) REVERT: C 213 ASP cc_start: 0.7819 (m-30) cc_final: 0.6867 (t70) REVERT: C 240 MET cc_start: 0.8254 (tpp) cc_final: 0.7523 (tpp) REVERT: C 326 ASP cc_start: 0.8241 (t0) cc_final: 0.8017 (t0) REVERT: C 940 ASP cc_start: 0.6689 (m-30) cc_final: 0.5726 (m-30) REVERT: C 1053 ASP cc_start: 0.9040 (m-30) cc_final: 0.8595 (t70) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1727 time to fit residues: 63.1210 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 : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 114 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 302 optimal weight: 7.9990 chunk 196 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 238 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN B 280 GLN ** 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 = 0.3752 r_free = 0.3752 target = 0.097793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072431 restraints weight = 99453.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074250 restraints weight = 56619.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075467 restraints weight = 39979.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076246 restraints weight = 31978.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076661 restraints weight = 27865.563| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1714 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= 0.154 Angle : 0.647 10.951 39114 Z= 0.311 Chirality : 0.045 0.366 4527 Planarity : 0.005 0.059 4950 Dihedral : 14.316 117.593 5085 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.14), residues: 3462 helix: 1.03 (0.21), residues: 708 sheet: -0.19 (0.18), residues: 750 loop : -0.91 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 822 TYR 0.018 0.001 TYR B1141 PHE 0.017 0.001 PHE C 366 TRP 0.008 0.001 TRP A 253 HIS 0.003 0.001 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.00340 (28542) covalent geometry : angle 0.60731 (38829) SS BOND : bond 0.00275 ( 48) SS BOND : angle 0.96383 ( 96) hydrogen bonds : bond 0.03842 ( 977) hydrogen bonds : angle 5.59203 ( 2574) link_ALPHA1-6 : bond 0.00873 ( 3) link_ALPHA1-6 : angle 1.40926 ( 9) link_BETA1-4 : bond 0.00348 ( 18) link_BETA1-4 : angle 2.66319 ( 54) link_BETA1-6 : bond 0.01660 ( 3) link_BETA1-6 : angle 1.57922 ( 9) link_NAG-ASN : bond 0.00420 ( 39) link_NAG-ASN : angle 3.60920 ( 117) *********************** 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 223 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9027 (tmm) cc_final: 0.8658 (tmm) REVERT: A 208 HIS cc_start: 0.7442 (t-90) cc_final: 0.6205 (t-90) REVERT: A 213 ASP cc_start: 0.8066 (m-30) cc_final: 0.6956 (t70) REVERT: A 292 TYR cc_start: 0.8356 (m-80) cc_final: 0.8003 (m-80) REVERT: A 326 ASP cc_start: 0.8234 (t0) cc_final: 0.8032 (t0) REVERT: A 580 ASP cc_start: 0.7674 (t0) cc_final: 0.7410 (t0) REVERT: A 757 MET cc_start: 0.8302 (mpp) cc_final: 0.7585 (mpp) REVERT: A 940 ASP cc_start: 0.6313 (m-30) cc_final: 0.5459 (m-30) REVERT: A 1053 ASP cc_start: 0.9177 (m-30) cc_final: 0.8744 (t70) REVERT: B 105 TYR cc_start: 0.8752 (m-80) cc_final: 0.8433 (m-80) REVERT: B 208 HIS cc_start: 0.6948 (t-90) cc_final: 0.5482 (t-90) REVERT: B 213 ASP cc_start: 0.8071 (m-30) cc_final: 0.7013 (t70) REVERT: B 940 ASP cc_start: 0.6586 (m-30) cc_final: 0.5516 (m-30) REVERT: B 1008 MET cc_start: 0.7281 (ppp) cc_final: 0.7035 (ppp) REVERT: B 1053 ASP cc_start: 0.9159 (m-30) cc_final: 0.8765 (t70) REVERT: B 1189 SER cc_start: 0.9104 (m) cc_final: 0.8751 (p) REVERT: C 105 TYR cc_start: 0.8697 (m-80) cc_final: 0.8416 (m-80) REVERT: C 240 MET cc_start: 0.8259 (tpp) cc_final: 0.7951 (tpt) REVERT: C 326 ASP cc_start: 0.8201 (t0) cc_final: 0.7993 (t0) REVERT: C 940 ASP cc_start: 0.7033 (m-30) cc_final: 0.5627 (m-30) REVERT: C 944 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 1053 ASP cc_start: 0.9011 (m-30) cc_final: 0.8596 (t70) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1670 time to fit residues: 63.7243 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 : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 274 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.098361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072944 restraints weight = 98574.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074832 restraints weight = 56311.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076057 restraints weight = 39521.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076843 restraints weight = 31634.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077277 restraints weight = 27566.129| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1855 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= 0.133 Angle : 0.619 11.480 39114 Z= 0.296 Chirality : 0.045 0.306 4527 Planarity : 0.004 0.059 4950 Dihedral : 13.396 118.544 5085 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.14), residues: 3462 helix: 1.10 (0.21), residues: 726 sheet: -0.23 (0.18), residues: 741 loop : -0.85 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 221 TYR 0.017 0.001 TYR C1153 PHE 0.018 0.001 PHE A 366 TRP 0.007 0.001 TRP A 253 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00298 (28542) covalent geometry : angle 0.58455 (38829) SS BOND : bond 0.00409 ( 48) SS BOND : angle 0.93407 ( 96) hydrogen bonds : bond 0.03518 ( 977) hydrogen bonds : angle 5.37020 ( 2574) link_ALPHA1-6 : bond 0.00889 ( 3) link_ALPHA1-6 : angle 1.43572 ( 9) link_BETA1-4 : bond 0.00319 ( 18) link_BETA1-4 : angle 2.59677 ( 54) link_BETA1-6 : bond 0.01757 ( 3) link_BETA1-6 : angle 1.73051 ( 9) link_NAG-ASN : bond 0.00414 ( 39) link_NAG-ASN : angle 3.24761 ( 117) *********************** 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 232 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9006 (tmm) cc_final: 0.8580 (tmm) REVERT: A 208 HIS cc_start: 0.7259 (t-90) cc_final: 0.6383 (t-170) REVERT: A 213 ASP cc_start: 0.8068 (m-30) cc_final: 0.6943 (t70) REVERT: A 240 MET cc_start: 0.8411 (tpt) cc_final: 0.8176 (tpp) REVERT: A 292 TYR cc_start: 0.8347 (m-80) cc_final: 0.8031 (m-80) REVERT: A 580 ASP cc_start: 0.7756 (t0) cc_final: 0.7505 (t0) REVERT: A 757 MET cc_start: 0.8357 (mpp) cc_final: 0.7620 (mpp) REVERT: A 940 ASP cc_start: 0.6479 (m-30) cc_final: 0.5617 (m-30) REVERT: A 1053 ASP cc_start: 0.9156 (m-30) cc_final: 0.8730 (t70) REVERT: B 84 MET cc_start: 0.8861 (tmm) cc_final: 0.8480 (tmm) REVERT: B 105 TYR cc_start: 0.8775 (m-80) cc_final: 0.8467 (m-80) REVERT: B 240 MET cc_start: 0.8077 (tpt) cc_final: 0.7774 (tpp) REVERT: B 326 ASP cc_start: 0.8278 (t0) cc_final: 0.8032 (t0) REVERT: B 940 ASP cc_start: 0.6667 (m-30) cc_final: 0.5557 (m-30) REVERT: B 943 MET cc_start: 0.8318 (tpt) cc_final: 0.8091 (tpt) REVERT: B 1053 ASP cc_start: 0.9158 (m-30) cc_final: 0.8741 (t70) REVERT: B 1189 SER cc_start: 0.9055 (m) cc_final: 0.8725 (p) REVERT: C 105 TYR cc_start: 0.8742 (m-80) cc_final: 0.8477 (m-80) REVERT: C 940 ASP cc_start: 0.7118 (m-30) cc_final: 0.5699 (m-30) REVERT: C 944 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8019 (mm-30) REVERT: C 1053 ASP cc_start: 0.9017 (m-30) cc_final: 0.8601 (t70) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1693 time to fit residues: 67.1659 Evaluate side-chains 177 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 32 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 516 GLN ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN B 208 HIS ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 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 516 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.096669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071156 restraints weight = 99787.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072991 restraints weight = 57265.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074208 restraints weight = 40388.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074982 restraints weight = 32481.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075418 restraints weight = 28381.950| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2198 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= 0.191 Angle : 0.665 11.389 39114 Z= 0.321 Chirality : 0.045 0.231 4527 Planarity : 0.005 0.059 4950 Dihedral : 13.128 119.442 5085 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.14), residues: 3462 helix: 1.32 (0.21), residues: 669 sheet: -0.30 (0.17), residues: 804 loop : -0.86 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 979 TYR 0.017 0.001 TYR A1153 PHE 0.018 0.001 PHE A 778 TRP 0.005 0.001 TRP A 960 HIS 0.006 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00423 (28542) covalent geometry : angle 0.63064 (38829) SS BOND : bond 0.00243 ( 48) SS BOND : angle 1.12606 ( 96) hydrogen bonds : bond 0.03761 ( 977) hydrogen bonds : angle 5.49964 ( 2574) link_ALPHA1-6 : bond 0.00631 ( 3) link_ALPHA1-6 : angle 1.48615 ( 9) link_BETA1-4 : bond 0.00331 ( 18) link_BETA1-4 : angle 2.47434 ( 54) link_BETA1-6 : bond 0.01893 ( 3) link_BETA1-6 : angle 1.96032 ( 9) link_NAG-ASN : bond 0.00408 ( 39) link_NAG-ASN : angle 3.37653 ( 117) *********************** 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 : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8491 (tpt) cc_final: 0.7844 (tpt) REVERT: A 292 TYR cc_start: 0.8328 (m-80) cc_final: 0.8032 (m-80) REVERT: A 326 ASP cc_start: 0.8321 (t0) cc_final: 0.8106 (t0) REVERT: A 580 ASP cc_start: 0.7846 (t0) cc_final: 0.7602 (t0) REVERT: A 757 MET cc_start: 0.8467 (mpp) cc_final: 0.7788 (mpp) REVERT: A 1008 MET cc_start: 0.7421 (ppp) cc_final: 0.6382 (ppp) REVERT: A 1053 ASP cc_start: 0.9183 (m-30) cc_final: 0.8736 (t70) REVERT: B 84 MET cc_start: 0.8897 (tmm) cc_final: 0.8532 (tmm) REVERT: B 105 TYR cc_start: 0.8818 (m-80) cc_final: 0.8541 (m-80) REVERT: B 208 HIS cc_start: 0.7457 (t70) cc_final: 0.6789 (t-90) REVERT: B 213 ASP cc_start: 0.7829 (m-30) cc_final: 0.6976 (t70) REVERT: B 240 MET cc_start: 0.8372 (tpt) cc_final: 0.8104 (tpp) REVERT: B 940 ASP cc_start: 0.7101 (m-30) cc_final: 0.5916 (m-30) REVERT: B 943 MET cc_start: 0.8370 (tpt) cc_final: 0.8127 (tpt) REVERT: B 1053 ASP cc_start: 0.9174 (m-30) cc_final: 0.8743 (t70) REVERT: B 1189 SER cc_start: 0.9073 (m) cc_final: 0.8784 (p) REVERT: C 208 HIS cc_start: 0.7166 (t-90) cc_final: 0.5861 (t-90) REVERT: C 213 ASP cc_start: 0.7720 (m-30) cc_final: 0.6858 (t70) REVERT: C 326 ASP cc_start: 0.8288 (t0) cc_final: 0.8004 (t0) REVERT: C 725 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7344 (mm-30) REVERT: C 731 LEU cc_start: 0.8800 (tp) cc_final: 0.8488 (tp) REVERT: C 1053 ASP cc_start: 0.9079 (m-30) cc_final: 0.8620 (t70) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1682 time to fit residues: 67.7830 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 : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 155 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 582 ASN A 772 GLN ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** A 857 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 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 796 GLN ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.094941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069551 restraints weight = 100396.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071291 restraints weight = 57540.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072431 restraints weight = 41014.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073059 restraints weight = 33193.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073583 restraints weight = 29419.546| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 28653 Z= 0.269 Angle : 0.743 11.855 39114 Z= 0.363 Chirality : 0.047 0.227 4527 Planarity : 0.005 0.059 4950 Dihedral : 13.087 119.267 5085 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.14), residues: 3462 helix: 0.94 (0.20), residues: 681 sheet: -0.75 (0.18), residues: 768 loop : -1.04 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 221 TYR 0.032 0.002 TYR C 105 PHE 0.041 0.002 PHE B 164 TRP 0.008 0.001 TRP A 960 HIS 0.006 0.002 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00594 (28542) covalent geometry : angle 0.70833 (38829) SS BOND : bond 0.00311 ( 48) SS BOND : angle 1.28436 ( 96) hydrogen bonds : bond 0.04214 ( 977) hydrogen bonds : angle 5.74616 ( 2574) link_ALPHA1-6 : bond 0.00402 ( 3) link_ALPHA1-6 : angle 1.52771 ( 9) link_BETA1-4 : bond 0.00387 ( 18) link_BETA1-4 : angle 2.46567 ( 54) link_BETA1-6 : bond 0.01700 ( 3) link_BETA1-6 : angle 1.97502 ( 9) link_NAG-ASN : bond 0.00396 ( 39) link_NAG-ASN : angle 3.63398 ( 117) *********************** 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 213 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9106 (tmm) cc_final: 0.8810 (tmm) REVERT: A 208 HIS cc_start: 0.7486 (t-90) cc_final: 0.6564 (t-170) REVERT: A 213 ASP cc_start: 0.8047 (m-30) cc_final: 0.6871 (t70) REVERT: A 240 MET cc_start: 0.8405 (tpt) cc_final: 0.7828 (tpt) REVERT: A 326 ASP cc_start: 0.8340 (t0) cc_final: 0.8038 (t0) REVERT: A 580 ASP cc_start: 0.8058 (t0) cc_final: 0.7854 (t0) REVERT: A 757 MET cc_start: 0.8409 (mpp) cc_final: 0.7862 (mpp) REVERT: A 1053 ASP cc_start: 0.9145 (m-30) cc_final: 0.8705 (t70) REVERT: B 84 MET cc_start: 0.8980 (tmm) cc_final: 0.8643 (tmm) REVERT: B 288 ASP cc_start: 0.7080 (m-30) cc_final: 0.6876 (m-30) REVERT: B 326 ASP cc_start: 0.8387 (t0) cc_final: 0.8148 (t0) REVERT: B 1053 ASP cc_start: 0.9153 (m-30) cc_final: 0.8729 (t70) REVERT: C 326 ASP cc_start: 0.8325 (t0) cc_final: 0.8010 (t0) REVERT: C 1053 ASP cc_start: 0.9086 (m-30) cc_final: 0.8669 (t70) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1650 time to fit residues: 60.7353 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 : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 263 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 249 optimal weight: 0.0040 chunk 147 optimal weight: 7.9990 chunk 265 optimal weight: 0.0670 chunk 11 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.5934 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.096951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072171 restraints weight = 99871.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074014 restraints weight = 57608.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075144 restraints weight = 40687.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075971 restraints weight = 32910.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076459 restraints weight = 28656.473| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2654 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 : 0.670 12.157 39114 Z= 0.321 Chirality : 0.045 0.258 4527 Planarity : 0.005 0.061 4950 Dihedral : 12.613 119.828 5085 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.14), residues: 3462 helix: 1.01 (0.20), residues: 702 sheet: -0.66 (0.17), residues: 786 loop : -0.94 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.032 0.001 TYR B 105 PHE 0.025 0.001 PHE C 164 TRP 0.008 0.001 TRP C 253 HIS 0.004 0.001 HIS C1122 Details of bonding type rmsd covalent geometry : bond 0.00367 (28542) covalent geometry : angle 0.63553 (38829) SS BOND : bond 0.00239 ( 48) SS BOND : angle 1.07971 ( 96) hydrogen bonds : bond 0.03696 ( 977) hydrogen bonds : angle 5.52571 ( 2574) link_ALPHA1-6 : bond 0.00471 ( 3) link_ALPHA1-6 : angle 1.42367 ( 9) link_BETA1-4 : bond 0.00296 ( 18) link_BETA1-4 : angle 2.49561 ( 54) link_BETA1-6 : bond 0.01662 ( 3) link_BETA1-6 : angle 2.01551 ( 9) link_NAG-ASN : bond 0.00391 ( 39) link_NAG-ASN : angle 3.40347 ( 117) *********************** 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 219 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9094 (tmm) cc_final: 0.8735 (tmm) REVERT: A 208 HIS cc_start: 0.7411 (t-90) cc_final: 0.6332 (t-170) REVERT: A 213 ASP cc_start: 0.8042 (m-30) cc_final: 0.6902 (t70) REVERT: A 240 MET cc_start: 0.8280 (tpt) cc_final: 0.7918 (tpt) REVERT: A 326 ASP cc_start: 0.8328 (t0) cc_final: 0.8071 (t0) REVERT: A 757 MET cc_start: 0.8207 (mpp) cc_final: 0.7360 (mpp) REVERT: A 1008 MET cc_start: 0.7489 (ppp) cc_final: 0.6329 (ppp) REVERT: A 1053 ASP cc_start: 0.9125 (m-30) cc_final: 0.8704 (t70) REVERT: B 84 MET cc_start: 0.9020 (tmm) cc_final: 0.8704 (tmm) REVERT: B 240 MET cc_start: 0.8253 (tpt) cc_final: 0.8035 (tpp) REVERT: B 326 ASP cc_start: 0.8280 (t0) cc_final: 0.8052 (t0) REVERT: B 1053 ASP cc_start: 0.9093 (m-30) cc_final: 0.8667 (t70) REVERT: C 326 ASP cc_start: 0.8271 (t0) cc_final: 0.7989 (t0) REVERT: C 725 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 777 TYR cc_start: 0.8185 (m-10) cc_final: 0.7967 (m-80) REVERT: C 1053 ASP cc_start: 0.9013 (m-30) cc_final: 0.8638 (t70) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1692 time to fit residues: 64.0478 Evaluate side-chains 160 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 147 optimal weight: 9.9990 chunk 179 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 250 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 344 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 288 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 A1016 ASN B 114 ASN B 226 ASN ** 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 280 GLN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C1016 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.098382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073706 restraints weight = 99960.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075581 restraints weight = 57257.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.076839 restraints weight = 40230.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.077626 restraints weight = 32153.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078044 restraints weight = 28023.415| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28653 Z= 0.122 Angle : 0.651 12.412 39114 Z= 0.311 Chirality : 0.045 0.255 4527 Planarity : 0.004 0.060 4950 Dihedral : 12.094 120.622 5085 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.14), residues: 3462 helix: 1.15 (0.21), residues: 702 sheet: -0.52 (0.18), residues: 783 loop : -0.89 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 887 TYR 0.024 0.001 TYR C 105 PHE 0.024 0.001 PHE C 164 TRP 0.010 0.001 TRP C 253 HIS 0.005 0.001 HIS C1122 Details of bonding type rmsd covalent geometry : bond 0.00276 (28542) covalent geometry : angle 0.61740 (38829) SS BOND : bond 0.00174 ( 48) SS BOND : angle 1.30794 ( 96) hydrogen bonds : bond 0.03491 ( 977) hydrogen bonds : angle 5.38559 ( 2574) link_ALPHA1-6 : bond 0.00527 ( 3) link_ALPHA1-6 : angle 1.37073 ( 9) link_BETA1-4 : bond 0.00250 ( 18) link_BETA1-4 : angle 2.54167 ( 54) link_BETA1-6 : bond 0.01638 ( 3) link_BETA1-6 : angle 2.14953 ( 9) link_NAG-ASN : bond 0.00408 ( 39) link_NAG-ASN : angle 3.17547 ( 117) *********************** 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 229 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9090 (tmm) cc_final: 0.8796 (tmm) REVERT: A 208 HIS cc_start: 0.7417 (t-90) cc_final: 0.6162 (t-90) REVERT: A 213 ASP cc_start: 0.7951 (m-30) cc_final: 0.6797 (t70) REVERT: A 240 MET cc_start: 0.8108 (tpt) cc_final: 0.7898 (tpt) REVERT: A 270 TYR cc_start: 0.6385 (m-80) cc_final: 0.6165 (m-80) REVERT: A 326 ASP cc_start: 0.8297 (t0) cc_final: 0.8077 (t0) REVERT: A 757 MET cc_start: 0.8203 (mpp) cc_final: 0.7347 (mpp) REVERT: A 1053 ASP cc_start: 0.9114 (m-30) cc_final: 0.8681 (t70) REVERT: B 84 MET cc_start: 0.9029 (tmm) cc_final: 0.8789 (tmm) REVERT: B 208 HIS cc_start: 0.7542 (t70) cc_final: 0.6414 (t-170) REVERT: B 213 ASP cc_start: 0.7903 (m-30) cc_final: 0.7070 (t70) REVERT: B 326 ASP cc_start: 0.8244 (t0) cc_final: 0.8043 (t0) REVERT: B 1053 ASP cc_start: 0.9091 (m-30) cc_final: 0.8666 (t70) REVERT: C 208 HIS cc_start: 0.7303 (t70) cc_final: 0.6078 (t-170) REVERT: C 213 ASP cc_start: 0.7663 (m-30) cc_final: 0.6762 (t0) REVERT: C 326 ASP cc_start: 0.8238 (t0) cc_final: 0.7976 (t0) REVERT: C 725 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7206 (mm-30) REVERT: C 1053 ASP cc_start: 0.9012 (m-30) cc_final: 0.8620 (t70) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1591 time to fit residues: 63.6308 Evaluate side-chains 176 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 173 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.0060 chunk 219 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 overall best weight: 3.6004 ------------------------------------------------------------------------------- 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 857 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 772 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.096516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.071945 restraints weight = 99759.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073710 restraints weight = 57191.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074905 restraints weight = 40524.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075580 restraints weight = 32612.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.076124 restraints weight = 28672.827| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 28653 Z= 0.202 Angle : 0.695 11.851 39114 Z= 0.337 Chirality : 0.045 0.214 4527 Planarity : 0.005 0.059 4950 Dihedral : 12.026 120.730 5085 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.14), residues: 3462 helix: 1.00 (0.20), residues: 702 sheet: -0.64 (0.18), residues: 780 loop : -0.94 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 887 TYR 0.025 0.002 TYR C 105 PHE 0.028 0.002 PHE C 164 TRP 0.007 0.001 TRP C 960 HIS 0.004 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00451 (28542) covalent geometry : angle 0.66296 (38829) SS BOND : bond 0.00242 ( 48) SS BOND : angle 1.22353 ( 96) hydrogen bonds : bond 0.03824 ( 977) hydrogen bonds : angle 5.51389 ( 2574) link_ALPHA1-6 : bond 0.00339 ( 3) link_ALPHA1-6 : angle 1.48042 ( 9) link_BETA1-4 : bond 0.00278 ( 18) link_BETA1-4 : angle 2.54492 ( 54) link_BETA1-6 : bond 0.01707 ( 3) link_BETA1-6 : angle 2.37440 ( 9) link_NAG-ASN : bond 0.00417 ( 39) link_NAG-ASN : angle 3.27248 ( 117) *********************** 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 217 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9200 (tmm) cc_final: 0.8871 (tmm) REVERT: A 208 HIS cc_start: 0.7449 (t-90) cc_final: 0.6369 (t-170) REVERT: A 213 ASP cc_start: 0.7997 (m-30) cc_final: 0.6798 (t70) REVERT: A 240 MET cc_start: 0.8248 (tpt) cc_final: 0.8010 (tpt) REVERT: A 270 TYR cc_start: 0.6389 (m-80) cc_final: 0.6169 (m-80) REVERT: A 326 ASP cc_start: 0.8314 (t0) cc_final: 0.8072 (t0) REVERT: A 731 LEU cc_start: 0.8605 (tp) cc_final: 0.8382 (tp) REVERT: A 757 MET cc_start: 0.8312 (mpp) cc_final: 0.7622 (mpp) REVERT: A 938 LEU cc_start: 0.8185 (tt) cc_final: 0.7520 (tp) REVERT: A 1008 MET cc_start: 0.7586 (ppp) cc_final: 0.6364 (ppp) REVERT: A 1053 ASP cc_start: 0.9119 (m-30) cc_final: 0.8672 (t70) REVERT: B 84 MET cc_start: 0.9100 (tmm) cc_final: 0.8856 (tmm) REVERT: B 326 ASP cc_start: 0.8255 (t0) cc_final: 0.8033 (t0) REVERT: B 940 ASP cc_start: 0.7071 (m-30) cc_final: 0.6543 (m-30) REVERT: B 1053 ASP cc_start: 0.9109 (m-30) cc_final: 0.8590 (t70) REVERT: C 288 ASP cc_start: 0.6966 (m-30) cc_final: 0.6743 (m-30) REVERT: C 326 ASP cc_start: 0.8223 (t0) cc_final: 0.7973 (t0) REVERT: C 1053 ASP cc_start: 0.9012 (m-30) cc_final: 0.8599 (t70) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1600 time to fit residues: 60.6453 Evaluate side-chains 160 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 317 optimal weight: 0.4980 chunk 331 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 857 GLN ** 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** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.095775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070993 restraints weight = 100375.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072785 restraints weight = 58101.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074012 restraints weight = 41091.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074704 restraints weight = 32970.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075216 restraints weight = 28965.428| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 28653 Z= 0.220 Angle : 0.716 11.824 39114 Z= 0.347 Chirality : 0.046 0.228 4527 Planarity : 0.005 0.061 4950 Dihedral : 11.863 120.548 5085 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3462 helix: 0.75 (0.20), residues: 720 sheet: -0.70 (0.18), residues: 756 loop : -1.08 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.025 0.002 TYR C 105 PHE 0.026 0.002 PHE C 164 TRP 0.008 0.001 TRP C 960 HIS 0.004 0.001 HIS B 836 Details of bonding type rmsd covalent geometry : bond 0.00489 (28542) covalent geometry : angle 0.68414 (38829) SS BOND : bond 0.00268 ( 48) SS BOND : angle 1.24188 ( 96) hydrogen bonds : bond 0.03949 ( 977) hydrogen bonds : angle 5.61649 ( 2574) link_ALPHA1-6 : bond 0.00252 ( 3) link_ALPHA1-6 : angle 1.53312 ( 9) link_BETA1-4 : bond 0.00275 ( 18) link_BETA1-4 : angle 2.62530 ( 54) link_BETA1-6 : bond 0.01708 ( 3) link_BETA1-6 : angle 2.62248 ( 9) link_NAG-ASN : bond 0.00410 ( 39) link_NAG-ASN : angle 3.31976 ( 117) ********************** 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 : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9249 (tmm) cc_final: 0.8947 (tmm) REVERT: A 208 HIS cc_start: 0.7562 (t-90) cc_final: 0.6384 (t-170) REVERT: A 213 ASP cc_start: 0.7833 (m-30) cc_final: 0.6783 (t70) REVERT: A 270 TYR cc_start: 0.6380 (m-80) cc_final: 0.6171 (m-80) REVERT: A 326 ASP cc_start: 0.8310 (t0) cc_final: 0.8063 (t0) REVERT: A 731 LEU cc_start: 0.8601 (tp) cc_final: 0.8390 (tp) REVERT: A 757 MET cc_start: 0.8322 (mpp) cc_final: 0.7655 (mpp) REVERT: A 1008 MET cc_start: 0.7697 (ppp) cc_final: 0.6499 (ppp) REVERT: A 1053 ASP cc_start: 0.9109 (m-30) cc_final: 0.8694 (t70) REVERT: B 84 MET cc_start: 0.9130 (tmm) cc_final: 0.8910 (tmm) REVERT: B 326 ASP cc_start: 0.8346 (t0) cc_final: 0.8111 (t0) REVERT: B 1053 ASP cc_start: 0.9065 (m-30) cc_final: 0.8550 (t70) REVERT: C 326 ASP cc_start: 0.8297 (t0) cc_final: 0.7998 (t0) REVERT: C 1053 ASP cc_start: 0.9001 (m-30) cc_final: 0.8586 (t70) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1666 time to fit residues: 62.0492 Evaluate side-chains 157 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 7 optimal weight: 30.0000 chunk 91 optimal weight: 0.1980 chunk 22 optimal weight: 6.9990 chunk 294 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 343 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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** ** 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 208 HIS ** 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 = 0.3746 r_free = 0.3746 target = 0.097112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.072483 restraints weight = 100191.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074282 restraints weight = 57282.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075511 restraints weight = 40434.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076290 restraints weight = 32444.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076754 restraints weight = 28277.897| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3031 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= 0.153 Angle : 0.677 12.268 39114 Z= 0.325 Chirality : 0.045 0.223 4527 Planarity : 0.004 0.062 4950 Dihedral : 11.317 120.128 5085 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.14), residues: 3462 helix: 0.83 (0.20), residues: 726 sheet: -0.66 (0.18), residues: 753 loop : -1.02 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 221 TYR 0.025 0.001 TYR C 105 PHE 0.024 0.001 PHE C 164 TRP 0.010 0.001 TRP C 253 HIS 0.004 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00346 (28542) covalent geometry : angle 0.64503 (38829) SS BOND : bond 0.00243 ( 48) SS BOND : angle 1.10805 ( 96) hydrogen bonds : bond 0.03645 ( 977) hydrogen bonds : angle 5.46744 ( 2574) link_ALPHA1-6 : bond 0.00352 ( 3) link_ALPHA1-6 : angle 1.43233 ( 9) link_BETA1-4 : bond 0.00260 ( 18) link_BETA1-4 : angle 2.69559 ( 54) link_BETA1-6 : bond 0.01819 ( 3) link_BETA1-6 : angle 2.72586 ( 9) link_NAG-ASN : bond 0.00392 ( 39) link_NAG-ASN : angle 3.17848 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4878.18 seconds wall clock time: 86 minutes 8.00 seconds (5168.00 seconds total)