Starting phenix.real_space_refine on Fri Feb 6 20:05:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5u_61152/02_2026/9j5u_61152_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5u_61152/02_2026/9j5u_61152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j5u_61152/02_2026/9j5u_61152_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5u_61152/02_2026/9j5u_61152_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j5u_61152/02_2026/9j5u_61152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5u_61152/02_2026/9j5u_61152.map" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 17233 2.51 5 N 4385 2.21 5 O 5390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27152 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8597 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 58, 'TRANS': 1044} Chain: "B" Number of atoms: 8597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8597 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 58, 'TRANS': 1044} Chain: "C" Number of atoms: 8597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8597 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 58, 'TRANS': 1044} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: "I" 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 161 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 167 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 141 Unusual residues: {'BLA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.08, per 1000 atoms: 0.22 Number of scatterers: 27152 At special positions: 0 Unit cell: (140.8, 148.72, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5390 8.00 N 4385 7.00 C 17233 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 162 " distance=2.04 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 368 " - pdb=" SG CYS A 421 " distance=2.06 Simple disulfide: pdb=" SG CYS A 380 " - pdb=" SG CYS A 510 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 575 " distance=2.04 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 636 " distance=2.07 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.04 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 740 " distance=2.03 Simple disulfide: pdb=" SG CYS A 723 " - pdb=" SG CYS A 729 " distance=2.03 Simple disulfide: pdb=" SG CYS A1012 " - pdb=" SG CYS A1023 " distance=2.02 Simple disulfide: pdb=" SG CYS A1062 " - pdb=" SG CYS A1106 " distance=2.01 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 368 " - pdb=" SG CYS B 421 " distance=2.07 Simple disulfide: pdb=" SG CYS B 380 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 465 " - pdb=" SG CYS B 473 " distance=2.02 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 636 " distance=2.04 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 740 " distance=2.03 Simple disulfide: pdb=" SG CYS B 723 " - pdb=" SG CYS B 729 " distance=2.03 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1023 " distance=2.03 Simple disulfide: pdb=" SG CYS B1062 " - pdb=" SG CYS B1106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.04 Simple disulfide: pdb=" SG CYS C 368 " - pdb=" SG CYS C 421 " distance=2.05 Simple disulfide: pdb=" SG CYS C 380 " - pdb=" SG CYS C 510 " distance=2.03 Simple disulfide: pdb=" SG CYS C 465 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 575 " distance=2.04 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 636 " distance=2.04 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 740 " distance=2.03 Simple disulfide: pdb=" SG CYS C 723 " - pdb=" SG CYS C 729 " distance=2.03 Simple disulfide: pdb=" SG CYS C1012 " - pdb=" SG CYS C1023 " distance=2.03 Simple disulfide: pdb=" SG CYS C1062 " - pdb=" SG CYS C1106 " distance=1.99 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA I 3 " - " MAN I 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A 114 " " NAG A1303 " - " ASN A 270 " " NAG A1304 " - " ASN A 601 " " NAG A1305 " - " ASN A 689 " " NAG A1306 " - " ASN A 697 " " NAG A1308 " - " ASN A 124 " " NAG B1302 " - " ASN B 65 " " NAG B1303 " - " ASN B 114 " " NAG B1304 " - " ASN B 270 " " NAG B1305 " - " ASN B 601 " " NAG B1306 " - " ASN B 689 " " NAG B1307 " - " ASN B 697 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C 270 " " NAG C1303 " - " ASN C 601 " " NAG C1304 " - " ASN C 689 " " NAG C1305 " - " ASN C 697 " " NAG C1306 " - " ASN C1114 " " NAG C1308 " - " ASN C 124 " " NAG D 1 " - " ASN A 161 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN B 161 " " NAG G 1 " - " ASN B 358 " " NAG H 1 " - " ASN C 161 " " NAG I 1 " - " ASN C 331 " " NAG J 1 " - " ASN C 358 " " NAG K 1 " - " ASN C 34 " " NAG L 1 " - " ASN C 114 " " NAG M 1 " - " ASN B1078 " " NAG N 1 " - " ASN C 228 " " NAG O 1 " - " ASN C 319 " " NAG P 1 " - " ASN C 781 " " NAG Q 1 " - " ASN C1078 " " NAG R 1 " - " ASN A 34 " " NAG S 1 " - " ASN A 228 " " NAG T 1 " - " ASN A 319 " " NAG U 1 " - " ASN A 358 " " NAG V 1 " - " ASN A 781 " " NAG W 1 " - " ASN A1078 " " NAG X 1 " - " ASN B 34 " " NAG Y 1 " - " ASN B 228 " " NAG Z 1 " - " ASN B 319 " " NAG b 1 " - " ASN B 781 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 47 sheets defined 22.7% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.636A pdb=" N VAL A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.584A pdb=" N VAL A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.522A pdb=" N LEU A 376 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN A 377 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 removed outlier: 4.810A pdb=" N HIS A 397 " --> pdb=" O ASP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 487 through 490 Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 611 through 614 removed outlier: 3.593A pdb=" N VAL A 614 " --> pdb=" O MET A 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 611 through 614' Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.795A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR A 621 " --> pdb=" O ASP A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 723 Processing helix chain 'A' and resid 726 through 734 Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 738 through 763 removed outlier: 3.609A pdb=" N ASN A 744 " --> pdb=" O CYS A 740 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 828 through 835 Processing helix chain 'A' and resid 846 through 859 removed outlier: 3.518A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 853 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'A' and resid 893 through 899 removed outlier: 3.721A pdb=" N TYR A 897 " --> pdb=" O GLN A 893 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.650A pdb=" N ASN A 905 " --> pdb=" O LYS A 901 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 928 through 944 removed outlier: 3.730A pdb=" N ILE A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 1012 removed outlier: 3.773A pdb=" N GLU A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 972 " --> pdb=" O GLU A 968 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 976 " --> pdb=" O GLN A 972 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 977 " --> pdb=" O ILE A 973 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A1001 " --> pdb=" O ASP A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.822A pdb=" N VAL B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.786A pdb=" N VAL B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 378 removed outlier: 3.581A pdb=" N LEU B 376 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASN B 377 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 removed outlier: 4.635A pdb=" N HIS B 397 " --> pdb=" O ASP B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 611 through 614 Processing helix chain 'B' and resid 615 through 623 removed outlier: 3.520A pdb=" N VAL B 620 " --> pdb=" O ASP B 617 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 623 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 723 Processing helix chain 'B' and resid 726 through 734 Processing helix chain 'B' and resid 735 through 737 No H-bonds generated for 'chain 'B' and resid 735 through 737' Processing helix chain 'B' and resid 740 through 763 removed outlier: 3.785A pdb=" N LEU B 747 " --> pdb=" O LEU B 743 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 803 removed outlier: 3.624A pdb=" N LEU B 801 " --> pdb=" O PRO B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 828 through 835 removed outlier: 3.812A pdb=" N ALA B 832 " --> pdb=" O ASP B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 859 removed outlier: 3.580A pdb=" N ALA B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 858 " --> pdb=" O THR B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 870 removed outlier: 3.743A pdb=" N GLY B 869 " --> pdb=" O PHE B 866 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 870 " --> pdb=" O THR B 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 866 through 870' Processing helix chain 'B' and resid 877 through 885 removed outlier: 3.707A pdb=" N ALA B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 884 " --> pdb=" O MET B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 898 removed outlier: 3.789A pdb=" N TYR B 897 " --> pdb=" O GLN B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 911 removed outlier: 3.511A pdb=" N ASN B 905 " --> pdb=" O LYS B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 removed outlier: 3.684A pdb=" N LEU B 918 " --> pdb=" O ILE B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 942 removed outlier: 4.045A pdb=" N GLN B 929 " --> pdb=" O LEU B 925 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 930 " --> pdb=" O GLY B 926 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 931 " --> pdb=" O LYS B 927 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 932 " --> pdb=" O LEU B 928 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 935 " --> pdb=" O VAL B 931 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 938 " --> pdb=" O GLN B 934 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 941 " --> pdb=" O ILE B 937 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 942 " --> pdb=" O ALA B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 1012 removed outlier: 3.824A pdb=" N GLU B 970 " --> pdb=" O PRO B 966 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 971 " --> pdb=" O PRO B 967 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN B 972 " --> pdb=" O GLU B 968 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG B 975 " --> pdb=" O VAL B 971 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 976 " --> pdb=" O GLN B 972 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 984 " --> pdb=" O ARG B 980 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B1001 " --> pdb=" O ASP B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1023 removed outlier: 3.766A pdb=" N PHE B1022 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS B1023 " --> pdb=" O VAL B1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1019 through 1023' Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.608A pdb=" N VAL C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.747A pdb=" N VAL C 355 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 378 removed outlier: 3.547A pdb=" N LEU C 376 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN C 377 " --> pdb=" O THR C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 4.367A pdb=" N HIS C 397 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 487 through 490 Processing helix chain 'C' and resid 604 through 610 Processing helix chain 'C' and resid 611 through 614 removed outlier: 3.738A pdb=" N VAL C 614 " --> pdb=" O MET C 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 611 through 614' Processing helix chain 'C' and resid 615 through 620 removed outlier: 3.558A pdb=" N ARG C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 620' Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 726 through 734 Processing helix chain 'C' and resid 735 through 737 No H-bonds generated for 'chain 'C' and resid 735 through 737' Processing helix chain 'C' and resid 741 through 763 removed outlier: 3.696A pdb=" N ARG C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 747 " --> pdb=" O LEU C 743 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 756 " --> pdb=" O VAL C 752 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 761 " --> pdb=" O ASN C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 806 removed outlier: 3.604A pdb=" N LEU C 801 " --> pdb=" O PRO C 797 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 806 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 817 removed outlier: 4.146A pdb=" N TYR C 817 " --> pdb=" O MET C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 835 removed outlier: 3.500A pdb=" N LYS C 834 " --> pdb=" O ILE C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 859 Processing helix chain 'C' and resid 877 through 888 removed outlier: 3.606A pdb=" N PHE C 886 " --> pdb=" O MET C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 899 removed outlier: 3.611A pdb=" N TYR C 897 " --> pdb=" O GLN C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 919 removed outlier: 3.512A pdb=" N ASN C 908 " --> pdb=" O ALA C 904 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 912 " --> pdb=" O ASN C 908 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 914 " --> pdb=" O ALA C 910 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN C 915 " --> pdb=" O ILE C 911 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 944 removed outlier: 3.961A pdb=" N GLN C 929 " --> pdb=" O LEU C 925 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 930 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL C 931 " --> pdb=" O LYS C 927 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 935 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 942 " --> pdb=" O ALA C 938 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 943 " --> pdb=" O LEU C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1012 removed outlier: 4.238A pdb=" N GLY C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 993 " --> pdb=" O THR C 989 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C1001 " --> pdb=" O ASP C 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 9.039A pdb=" N ASN A 65 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N HIS A 257 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS A 200 " --> pdb=" O PRO A 219 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N TYR A 202 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N LEU A 217 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG A 38 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N LEU A 217 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE A 40 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 34 removed outlier: 4.149A pdb=" N GLN A 72 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 80 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87 removed outlier: 4.359A pdb=" N GLY A 105 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG A 104 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A 123 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N TYR A 134 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N CYS A 162 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASN A 136 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ASN A 160 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N CYS A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N ARG A 158 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU A 140 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR A 156 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 303 removed outlier: 4.883A pdb=" N VAL A 580 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 316 removed outlier: 5.290A pdb=" N ASP A 559 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 346 removed outlier: 3.613A pdb=" N GLU A 342 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 384 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 383 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 365 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN A 426 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE A 363 " --> pdb=" O ASN A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.620A pdb=" N CYS A 349 " --> pdb=" O CYS A 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 437 through 439 Processing sheet with id=AB1, first strand: chain 'A' and resid 458 through 459 Processing sheet with id=AB2, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.187A pdb=" N THR A 641 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N THR A 676 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 659 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.379A pdb=" N GLU A 681 " --> pdb=" O ILE C 768 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 691 through 708 removed outlier: 6.813A pdb=" N SER A 691 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A1056 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A 693 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN A1054 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP A1052 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A1030 " --> pdb=" O VAL A1045 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR A1047 " --> pdb=" O HIS A1028 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS A1028 " --> pdb=" O TYR A1047 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 691 through 708 removed outlier: 6.813A pdb=" N SER A 691 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A1056 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A 693 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN A1054 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP A1052 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR A1056 " --> pdb=" O THR A1077 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1058 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A1075 " --> pdb=" O ALA A1058 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN A1086 " --> pdb=" O GLN A1091 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLN A1091 " --> pdb=" O GLN A1086 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 716 removed outlier: 4.422A pdb=" N LYS A 713 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB8, first strand: chain 'A' and resid 1100 through 1105 removed outlier: 5.178A pdb=" N ALA A1067 " --> pdb=" O SER A1103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.093A pdb=" N LEU B 196 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 222 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 198 " --> pdb=" O MET B 220 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N TYR B 202 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N VAL B 216 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE B 40 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 Processing sheet with id=AC2, first strand: chain 'B' and resid 86 through 87 removed outlier: 4.067A pdb=" N GLY B 105 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ARG B 104 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 134 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS B 162 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ASN B 136 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASN B 160 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N CYS B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N ARG B 158 " --> pdb=" O CYS B 138 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLU B 140 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR B 156 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER B 146 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 299 through 303 removed outlier: 4.923A pdb=" N VAL B 580 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 313 through 316 removed outlier: 5.313A pdb=" N ASP B 559 " --> pdb=" O ILE B 572 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 342 through 346 removed outlier: 3.624A pdb=" N GLU B 342 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 384 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 383 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.577A pdb=" N CYS B 349 " --> pdb=" O CYS B 510 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 437 through 439 Processing sheet with id=AC8, first strand: chain 'B' and resid 458 through 459 Processing sheet with id=AC9, first strand: chain 'B' and resid 641 through 642 removed outlier: 6.123A pdb=" N THR B 641 " --> pdb=" O ALA B 674 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR B 676 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA B 659 " --> pdb=" O PRO B 652 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 691 through 708 removed outlier: 6.751A pdb=" N SER B 691 " --> pdb=" O THR B1056 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B1056 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 693 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B1054 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP B1052 " --> pdb=" O PRO B 695 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR B1047 " --> pdb=" O HIS B1028 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS B1028 " --> pdb=" O TYR B1047 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 691 through 708 removed outlier: 6.751A pdb=" N SER B 691 " --> pdb=" O THR B1056 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B1056 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 693 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B1054 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP B1052 " --> pdb=" O PRO B 695 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B1056 " --> pdb=" O THR B1077 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B1058 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE B1075 " --> pdb=" O ALA B1058 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 713 through 716 removed outlier: 4.508A pdb=" N LYS B 713 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 767 through 768 Processing sheet with id=AD5, first strand: chain 'B' and resid 1100 through 1105 removed outlier: 5.127A pdb=" N ALA B1067 " --> pdb=" O SER B1103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 34 removed outlier: 8.559A pdb=" N ASN C 65 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N HIS C 257 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS C 200 " --> pdb=" O PRO C 219 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N TYR C 202 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N LEU C 217 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE C 40 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 59 Processing sheet with id=AD8, first strand: chain 'C' and resid 73 through 74 removed outlier: 3.646A pdb=" N ILE C 74 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 86 through 87 removed outlier: 4.415A pdb=" N GLY C 105 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG C 104 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN C 123 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE C 128 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN C 165 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL C 132 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR C 134 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN C 161 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASN C 136 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA C 159 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N CYS C 138 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASP C 157 " --> pdb=" O CYS C 138 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU C 140 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C 155 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET C 142 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER C 153 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA C 144 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR C 151 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 299 through 302 Processing sheet with id=AE2, first strand: chain 'C' and resid 313 through 316 removed outlier: 5.463A pdb=" N ASP C 559 " --> pdb=" O ILE C 572 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.704A pdb=" N GLU C 342 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL C 384 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C 383 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASN C 426 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE C 363 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 349 through 350 removed outlier: 6.646A pdb=" N CYS C 349 " --> pdb=" O CYS C 510 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 437 through 439 Processing sheet with id=AE6, first strand: chain 'C' and resid 458 through 459 Processing sheet with id=AE7, first strand: chain 'C' and resid 641 through 647 removed outlier: 6.194A pdb=" N THR C 641 " --> pdb=" O ALA C 674 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR C 676 " --> pdb=" O THR C 641 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ASP C 643 " --> pdb=" O THR C 676 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 659 " --> pdb=" O PRO C 652 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 691 through 708 removed outlier: 6.499A pdb=" N SER C 691 " --> pdb=" O THR C1056 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C1056 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 693 " --> pdb=" O ASN C1054 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1054 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP C1052 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET C1030 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR C1047 " --> pdb=" O HIS C1028 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS C1028 " --> pdb=" O TYR C1047 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 691 through 708 removed outlier: 6.499A pdb=" N SER C 691 " --> pdb=" O THR C1056 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C1056 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 693 " --> pdb=" O ASN C1054 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1054 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP C1052 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR C1056 " --> pdb=" O THR C1077 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C1077 " --> pdb=" O THR C1056 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN C1086 " --> pdb=" O GLN C1091 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLN C1091 " --> pdb=" O GLN C1086 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 713 through 716 removed outlier: 4.639A pdb=" N LYS C 713 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1100 through 1105 removed outlier: 5.097A pdb=" N ALA C1067 " --> pdb=" O SER C1103 " (cutoff:3.500A) 954 hydrogen bonds defined for protein. 2577 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: 6.13 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5586 1.33 - 1.46: 9536 1.46 - 1.60: 12459 1.60 - 1.74: 0 1.74 - 1.88: 198 Bond restraints: 27779 Sorted by residual: bond pdb=" N VAL B1013 " pdb=" CA VAL B1013 " ideal model delta sigma weight residual 1.454 1.514 -0.060 1.19e-02 7.06e+03 2.51e+01 bond pdb=" N VAL C 55 " pdb=" CA VAL C 55 " ideal model delta sigma weight residual 1.454 1.489 -0.034 7.70e-03 1.69e+04 1.97e+01 bond pdb=" N ALA B 183 " pdb=" CA ALA B 183 " ideal model delta sigma weight residual 1.455 1.506 -0.050 1.18e-02 7.18e+03 1.81e+01 bond pdb=" C1D BLA A1307 " pdb=" CHD BLA A1307 " ideal model delta sigma weight residual 1.440 1.358 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" N GLN B 893 " pdb=" CA GLN B 893 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.33e-02 5.65e+03 1.52e+01 ... (remaining 27774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 36181 2.68 - 5.36: 1500 5.36 - 8.04: 141 8.04 - 10.72: 18 10.72 - 13.40: 1 Bond angle restraints: 37841 Sorted by residual: angle pdb=" N VAL C 971 " pdb=" CA VAL C 971 " pdb=" C VAL C 971 " ideal model delta sigma weight residual 112.96 105.13 7.83 1.00e+00 1.00e+00 6.13e+01 angle pdb=" C VAL C 73 " pdb=" CA VAL C 73 " pdb=" CB VAL C 73 " ideal model delta sigma weight residual 111.35 119.26 -7.91 1.09e+00 8.42e-01 5.27e+01 angle pdb=" N ASN C 75 " pdb=" CA ASN C 75 " pdb=" C ASN C 75 " ideal model delta sigma weight residual 111.36 118.88 -7.52 1.09e+00 8.42e-01 4.76e+01 angle pdb=" N LYS C 794 " pdb=" CA LYS C 794 " pdb=" C LYS C 794 " ideal model delta sigma weight residual 112.57 105.05 7.52 1.13e+00 7.83e-01 4.43e+01 angle pdb=" N VAL C 73 " pdb=" CA VAL C 73 " pdb=" C VAL C 73 " ideal model delta sigma weight residual 108.12 99.25 8.87 1.34e+00 5.57e-01 4.38e+01 ... (remaining 37836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 15863 24.05 - 48.10: 1384 48.10 - 72.15: 295 72.15 - 96.19: 86 96.19 - 120.24: 71 Dihedral angle restraints: 17699 sinusoidal: 8039 harmonic: 9660 Sorted by residual: dihedral pdb=" CB CYS C 602 " pdb=" SG CYS C 602 " pdb=" SG CYS C 636 " pdb=" CB CYS C 636 " ideal model delta sinusoidal sigma weight residual -86.00 -3.43 -82.57 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS C 523 " pdb=" SG CYS C 523 " pdb=" SG CYS C 575 " pdb=" CB CYS C 575 " ideal model delta sinusoidal sigma weight residual -86.00 -20.27 -65.73 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual -86.00 -24.51 -61.49 1 1.00e+01 1.00e-02 5.02e+01 ... (remaining 17696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 4429 0.189 - 0.378: 77 0.378 - 0.566: 6 0.566 - 0.755: 2 0.755 - 0.944: 2 Chirality restraints: 4516 Sorted by residual: chirality pdb=" C1 BMA L 2 " pdb=" O4 NAG L 1 " pdb=" C2 BMA L 2 " pdb=" O5 BMA L 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-02 2.50e+03 2.14e+03 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-02 2.50e+03 4.72e+02 chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 2.01 0.39 2.00e-02 2.50e+03 3.73e+02 ... (remaining 4513 not shown) Planarity restraints: 4822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1307 " -0.701 2.00e-02 2.50e+03 5.75e-01 8.26e+03 pdb=" C1A BLA A1307 " 1.147 2.00e-02 2.50e+03 pdb=" C1D BLA A1307 " -0.158 2.00e-02 2.50e+03 pdb=" C2D BLA A1307 " 0.177 2.00e-02 2.50e+03 pdb=" C3D BLA A1307 " -0.290 2.00e-02 2.50e+03 pdb=" C4D BLA A1307 " -0.423 2.00e-02 2.50e+03 pdb=" CAD BLA A1307 " -0.578 2.00e-02 2.50e+03 pdb=" CHA BLA A1307 " -0.118 2.00e-02 2.50e+03 pdb=" CHD BLA A1307 " 0.033 2.00e-02 2.50e+03 pdb=" CMD BLA A1307 " 0.910 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA B1309 " -0.426 2.00e-02 2.50e+03 4.47e-01 5.00e+03 pdb=" OB BLA B1309 " -0.074 2.00e-02 2.50e+03 pdb=" C1B BLA B1309 " -0.291 2.00e-02 2.50e+03 pdb=" C2B BLA B1309 " -0.216 2.00e-02 2.50e+03 pdb=" C3B BLA B1309 " 0.188 2.00e-02 2.50e+03 pdb=" C4A BLA B1309 " 0.893 2.00e-02 2.50e+03 pdb=" C4B BLA B1309 " -0.099 2.00e-02 2.50e+03 pdb=" CAB BLA B1309 " 0.738 2.00e-02 2.50e+03 pdb=" CHB BLA B1309 " -0.217 2.00e-02 2.50e+03 pdb=" CMB BLA B1309 " -0.498 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1307 " 0.075 2.00e-02 2.50e+03 2.40e-01 1.44e+03 pdb=" C1D BLA A1307 " 0.196 2.00e-02 2.50e+03 pdb=" C2C BLA A1307 " -0.046 2.00e-02 2.50e+03 pdb=" C3C BLA A1307 " 0.078 2.00e-02 2.50e+03 pdb=" C4C BLA A1307 " -0.109 2.00e-02 2.50e+03 pdb=" CAC BLA A1307 " 0.315 2.00e-02 2.50e+03 pdb=" CHD BLA A1307 " -0.541 2.00e-02 2.50e+03 pdb=" CMC BLA A1307 " -0.259 2.00e-02 2.50e+03 pdb=" NC BLA A1307 " 0.221 2.00e-02 2.50e+03 pdb=" OC BLA A1307 " 0.070 2.00e-02 2.50e+03 ... (remaining 4819 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 236 2.60 - 3.17: 21613 3.17 - 3.75: 38633 3.75 - 4.32: 55494 4.32 - 4.90: 92287 Nonbonded interactions: 208263 Sorted by model distance: nonbonded pdb=" NE2 GLN A 334 " pdb=" O PHE A 335 " model vdw 2.021 3.120 nonbonded pdb=" NH1 ARG B 442 " pdb=" OD2 ASP B 452 " model vdw 2.204 3.120 nonbonded pdb=" NE2 GLN C 72 " pdb=" O VAL C 73 " model vdw 2.235 3.120 nonbonded pdb=" O PRO B 708 " pdb=" OG SER B1001 " model vdw 2.239 3.040 nonbonded pdb=" O SER B 855 " pdb=" OG SER B 859 " model vdw 2.239 3.040 ... (remaining 208258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 1118 or resid 1302 through 1306)) selection = (chain 'B' and (resid 16 through 1118 or resid 1302 through 1306)) selection = (chain 'C' and (resid 16 through 1118 or resid 1302 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'N' selection = chain 'S' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'b' and resid 1) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.270 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.008 0.082 27905 Z= 0.473 Angle : 1.245 19.454 38180 Z= 0.739 Chirality : 0.074 0.944 4516 Planarity : 0.022 0.575 4778 Dihedral : 19.871 120.242 11384 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.96 % Favored : 91.55 % Rotamer: Outliers : 5.66 % Allowed : 26.56 % Favored : 67.77 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -2.61 (0.13), residues: 3303 helix: -2.33 (0.18), residues: 711 sheet: 0.23 (0.19), residues: 726 loop : -2.40 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 166 TYR 0.025 0.002 TYR B 197 PHE 0.027 0.002 PHE C1069 TRP 0.019 0.002 TRP A 76 HIS 0.008 0.002 HIS A1063 Details of bonding type rmsd covalent geometry : bond 0.00799 (27779) covalent geometry : angle 1.16468 (37841) SS BOND : bond 0.01294 ( 39) SS BOND : angle 2.71210 ( 78) hydrogen bonds : bond 0.21447 ( 914) hydrogen bonds : angle 7.86947 ( 2577) link_ALPHA1-3 : bond 0.02747 ( 6) link_ALPHA1-3 : angle 3.94232 ( 18) link_ALPHA1-6 : bond 0.00009 ( 1) link_ALPHA1-6 : angle 2.08019 ( 3) link_BETA1-4 : bond 0.02970 ( 36) link_BETA1-4 : angle 5.11465 ( 108) link_NAG-ASN : bond 0.00911 ( 44) link_NAG-ASN : angle 5.60104 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 312 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6469 (m) REVERT: C 1009 MET cc_start: 0.8134 (tpp) cc_final: 0.7862 (tpp) outliers start: 164 outliers final: 44 residues processed: 436 average time/residue: 0.6615 time to fit residues: 335.4664 Evaluate side-chains 210 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 966 PRO Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 819 ASP Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 334 GLN A 471 HIS A 764 GLN A 784 GLN A 899 ASN A 908 ASN A 949 ASN A 982 GLN A1081 HIS B 30 GLN B 136 ASN B 200 HIS B 887 ASN B 893 GLN B 902 GLN B 949 ASN B1016 GLN B1081 HIS C 70 GLN C 101 ASN C 136 ASN C 245 ASN C 934 GLN C 940 ASN C 945 GLN C 972 GLN C1081 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.057087 restraints weight = 58974.667| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.39 r_work: 0.2705 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27905 Z= 0.161 Angle : 0.820 18.137 38180 Z= 0.390 Chirality : 0.049 0.256 4516 Planarity : 0.005 0.065 4778 Dihedral : 12.935 98.002 5569 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 4.94 % Allowed : 25.11 % Favored : 69.95 % 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 are not related in a simple way. whole: -2.16 (0.14), residues: 3303 helix: -1.45 (0.19), residues: 726 sheet: 0.33 (0.18), residues: 750 loop : -2.28 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 104 TYR 0.021 0.001 TYR B 577 PHE 0.023 0.001 PHE B 907 TRP 0.012 0.001 TRP B 76 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00356 (27779) covalent geometry : angle 0.78345 (37841) SS BOND : bond 0.00511 ( 39) SS BOND : angle 1.45364 ( 78) hydrogen bonds : bond 0.05769 ( 914) hydrogen bonds : angle 5.91396 ( 2577) link_ALPHA1-3 : bond 0.01137 ( 6) link_ALPHA1-3 : angle 2.62551 ( 18) link_ALPHA1-6 : bond 0.00667 ( 1) link_ALPHA1-6 : angle 1.65948 ( 3) link_BETA1-4 : bond 0.00702 ( 36) link_BETA1-4 : angle 2.70356 ( 108) link_NAG-ASN : bond 0.00438 ( 44) link_NAG-ASN : angle 3.21510 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 177 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 53 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8857 (m) REVERT: A 691 SER cc_start: 0.9552 (OUTLIER) cc_final: 0.9312 (t) REVERT: A 968 GLU cc_start: 0.8900 (tp30) cc_final: 0.8665 (tp30) REVERT: A 970 GLU cc_start: 0.8207 (mp0) cc_final: 0.8004 (mp0) REVERT: A 1105 ASN cc_start: 0.9093 (p0) cc_final: 0.8797 (p0) REVERT: B 32 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: B 133 CYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7109 (m) REVERT: C 70 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8566 (pp30) REVERT: C 327 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8792 (t0) outliers start: 143 outliers final: 57 residues processed: 300 average time/residue: 0.5785 time to fit residues: 206.5503 Evaluate side-chains 209 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 146 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 887 ASN Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 775 LYS Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1074 VAL Chi-restraints excluded: chain C residue 1085 THR Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 129 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A 624 ASN A 906 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 875 GLN B 982 GLN B1081 HIS B1114 ASN C 624 ASN C 881 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.053469 restraints weight = 59517.500| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.39 r_work: 0.2613 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 27905 Z= 0.232 Angle : 0.789 13.763 38180 Z= 0.387 Chirality : 0.050 0.246 4516 Planarity : 0.005 0.054 4778 Dihedral : 10.194 101.486 5534 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 4.77 % Allowed : 22.69 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.14), residues: 3303 helix: -0.71 (0.20), residues: 705 sheet: 0.26 (0.18), residues: 774 loop : -2.18 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 666 TYR 0.019 0.002 TYR A 253 PHE 0.020 0.002 PHE B 907 TRP 0.010 0.001 TRP A 76 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00556 (27779) covalent geometry : angle 0.75608 (37841) SS BOND : bond 0.00621 ( 39) SS BOND : angle 1.87048 ( 78) hydrogen bonds : bond 0.06217 ( 914) hydrogen bonds : angle 5.63299 ( 2577) link_ALPHA1-3 : bond 0.01089 ( 6) link_ALPHA1-3 : angle 2.12499 ( 18) link_ALPHA1-6 : bond 0.01162 ( 1) link_ALPHA1-6 : angle 1.18795 ( 3) link_BETA1-4 : bond 0.00800 ( 36) link_BETA1-4 : angle 2.56411 ( 108) link_NAG-ASN : bond 0.00408 ( 44) link_NAG-ASN : angle 2.81813 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 149 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 187 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.8040 (mm-40) REVERT: A 691 SER cc_start: 0.9543 (OUTLIER) cc_final: 0.9261 (t) REVERT: A 816 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6374 (mm110) REVERT: A 896 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9029 (tt) REVERT: A 968 GLU cc_start: 0.9055 (tp30) cc_final: 0.8782 (tp30) REVERT: A 970 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: A 1093 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 1095 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8409 (mt) REVERT: A 1105 ASN cc_start: 0.9167 (p0) cc_final: 0.8749 (p0) REVERT: B 32 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7054 (tm130) REVERT: B 142 MET cc_start: 0.8380 (ptp) cc_final: 0.8059 (pp-130) REVERT: B 143 PHE cc_start: 0.8314 (m-80) cc_final: 0.7695 (m-80) REVERT: B 784 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8549 (pp30) REVERT: B 999 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8059 (tpm-80) REVERT: C 142 MET cc_start: 0.8153 (mtp) cc_final: 0.7879 (ttm) REVERT: C 327 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8886 (t0) REVERT: C 681 GLU cc_start: 0.8280 (mp0) cc_final: 0.7878 (pm20) outliers start: 138 outliers final: 65 residues processed: 264 average time/residue: 0.5688 time to fit residues: 179.9753 Evaluate side-chains 213 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 137 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 775 LYS Chi-restraints excluded: chain C residue 793 SER Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 982 GLN Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1085 THR Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1113 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 189 optimal weight: 0.0270 chunk 199 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 398 GLN A 741 GLN A 982 GLN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN B 598 GLN B1081 HIS B1114 ASN C 70 GLN C 136 ASN C 906 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.055245 restraints weight = 59187.631| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.40 r_work: 0.2655 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27905 Z= 0.126 Angle : 0.683 12.105 38180 Z= 0.330 Chirality : 0.046 0.216 4516 Planarity : 0.004 0.050 4778 Dihedral : 8.840 98.149 5531 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 3.73 % Allowed : 22.56 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3303 helix: -0.23 (0.20), residues: 711 sheet: 0.34 (0.18), residues: 777 loop : -2.08 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 666 TYR 0.016 0.001 TYR C1047 PHE 0.022 0.001 PHE A1101 TRP 0.009 0.001 TRP B 425 HIS 0.006 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00279 (27779) covalent geometry : angle 0.65391 (37841) SS BOND : bond 0.00526 ( 39) SS BOND : angle 1.32055 ( 78) hydrogen bonds : bond 0.04787 ( 914) hydrogen bonds : angle 5.42107 ( 2577) link_ALPHA1-3 : bond 0.01147 ( 6) link_ALPHA1-3 : angle 2.19347 ( 18) link_ALPHA1-6 : bond 0.00973 ( 1) link_ALPHA1-6 : angle 1.21680 ( 3) link_BETA1-4 : bond 0.00645 ( 36) link_BETA1-4 : angle 2.31822 ( 108) link_NAG-ASN : bond 0.00301 ( 44) link_NAG-ASN : angle 2.48887 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 157 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8433 (mtp180) REVERT: A 97 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7925 (mp) REVERT: A 484 SER cc_start: 0.9507 (OUTLIER) cc_final: 0.9284 (p) REVERT: A 741 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: A 816 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6328 (mm110) REVERT: A 896 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8982 (tt) REVERT: A 968 GLU cc_start: 0.9099 (tp30) cc_final: 0.8808 (tp30) REVERT: A 970 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: A 1093 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 1105 ASN cc_start: 0.9203 (p0) cc_final: 0.8759 (p0) REVERT: B 238 MET cc_start: 0.5643 (tpt) cc_final: 0.5313 (tpt) REVERT: B 266 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8221 (tp30) REVERT: B 709 VAL cc_start: 0.9367 (OUTLIER) cc_final: 0.9090 (t) REVERT: B 999 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8094 (tpm-80) REVERT: C 681 GLU cc_start: 0.8294 (mp0) cc_final: 0.7754 (pm20) outliers start: 108 outliers final: 54 residues processed: 242 average time/residue: 0.6037 time to fit residues: 172.8181 Evaluate side-chains 203 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 139 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain C residue 982 GLN Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 3.9990 chunk 239 optimal weight: 0.0980 chunk 318 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS C 171 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.053243 restraints weight = 59343.767| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.40 r_work: 0.2609 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27905 Z= 0.200 Angle : 0.715 11.180 38180 Z= 0.351 Chirality : 0.048 0.229 4516 Planarity : 0.005 0.044 4778 Dihedral : 8.398 96.075 5530 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 4.08 % Allowed : 21.35 % Favored : 74.58 % 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 are not related in a simple way. whole: -1.45 (0.14), residues: 3303 helix: 0.08 (0.20), residues: 726 sheet: 0.32 (0.18), residues: 777 loop : -2.10 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.018 0.001 TYR B1047 PHE 0.018 0.001 PHE A1101 TRP 0.009 0.001 TRP B 425 HIS 0.006 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00482 (27779) covalent geometry : angle 0.68458 (37841) SS BOND : bond 0.00413 ( 39) SS BOND : angle 1.71733 ( 78) hydrogen bonds : bond 0.05638 ( 914) hydrogen bonds : angle 5.43324 ( 2577) link_ALPHA1-3 : bond 0.01105 ( 6) link_ALPHA1-3 : angle 2.34121 ( 18) link_ALPHA1-6 : bond 0.01113 ( 1) link_ALPHA1-6 : angle 1.13455 ( 3) link_BETA1-4 : bond 0.00671 ( 36) link_BETA1-4 : angle 2.30565 ( 108) link_NAG-ASN : bond 0.00320 ( 44) link_NAG-ASN : angle 2.56694 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 141 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 691 SER cc_start: 0.9554 (OUTLIER) cc_final: 0.9255 (t) REVERT: A 741 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8707 (tm-30) REVERT: A 770 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8620 (pmtt) REVERT: A 816 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6332 (mm110) REVERT: A 896 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8988 (tt) REVERT: A 968 GLU cc_start: 0.9115 (tp30) cc_final: 0.8859 (tp30) REVERT: A 970 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: A 1093 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7438 (tm-30) REVERT: A 1105 ASN cc_start: 0.9196 (p0) cc_final: 0.8767 (p0) REVERT: B 142 MET cc_start: 0.7795 (mtt) cc_final: 0.7225 (tpp) REVERT: B 238 MET cc_start: 0.5170 (tpt) cc_final: 0.3786 (ppp) REVERT: B 266 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8244 (tp30) REVERT: B 491 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8972 (mt0) REVERT: B 968 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8401 (tp30) REVERT: B 999 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8082 (tpm-80) REVERT: C 641 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9140 (p) REVERT: C 681 GLU cc_start: 0.8341 (mp0) cc_final: 0.7923 (pm20) REVERT: C 813 PHE cc_start: 0.5142 (OUTLIER) cc_final: 0.4579 (t80) outliers start: 118 outliers final: 62 residues processed: 239 average time/residue: 0.5534 time to fit residues: 157.4949 Evaluate side-chains 206 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 770 LYS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain C residue 982 GLN Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1113 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 227 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 324 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN A 982 GLN B1081 HIS C 171 ASN C 881 GLN C 913 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.053446 restraints weight = 59178.037| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.40 r_work: 0.2614 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27905 Z= 0.173 Angle : 0.681 10.667 38180 Z= 0.336 Chirality : 0.047 0.220 4516 Planarity : 0.004 0.042 4778 Dihedral : 8.016 93.871 5529 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 3.73 % Allowed : 21.35 % Favored : 74.92 % 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 are not related in a simple way. whole: -1.33 (0.14), residues: 3303 helix: 0.30 (0.20), residues: 726 sheet: 0.36 (0.18), residues: 777 loop : -2.05 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.017 0.001 TYR B1047 PHE 0.023 0.001 PHE A1101 TRP 0.010 0.001 TRP B 425 HIS 0.006 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00414 (27779) covalent geometry : angle 0.65258 (37841) SS BOND : bond 0.00355 ( 39) SS BOND : angle 1.59741 ( 78) hydrogen bonds : bond 0.05261 ( 914) hydrogen bonds : angle 5.38079 ( 2577) link_ALPHA1-3 : bond 0.01093 ( 6) link_ALPHA1-3 : angle 2.17544 ( 18) link_ALPHA1-6 : bond 0.01058 ( 1) link_ALPHA1-6 : angle 1.22300 ( 3) link_BETA1-4 : bond 0.00620 ( 36) link_BETA1-4 : angle 2.15273 ( 108) link_NAG-ASN : bond 0.00286 ( 44) link_NAG-ASN : angle 2.45620 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 140 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 691 SER cc_start: 0.9556 (OUTLIER) cc_final: 0.9262 (t) REVERT: A 741 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: A 770 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8616 (pmtt) REVERT: A 816 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6265 (mm110) REVERT: A 846 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8586 (p) REVERT: A 875 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8707 (pt0) REVERT: A 896 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8960 (tt) REVERT: A 968 GLU cc_start: 0.9107 (tp30) cc_final: 0.8841 (tp30) REVERT: A 970 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: A 1093 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 1105 ASN cc_start: 0.9221 (p0) cc_final: 0.8783 (p0) REVERT: B 142 MET cc_start: 0.7699 (mtt) cc_final: 0.7216 (tpp) REVERT: B 236 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6782 (mmt) REVERT: B 238 MET cc_start: 0.5096 (tpt) cc_final: 0.3820 (ppp) REVERT: B 266 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8255 (tp30) REVERT: B 968 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8372 (tp30) REVERT: B 999 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8067 (tpm-80) REVERT: C 681 GLU cc_start: 0.8395 (mp0) cc_final: 0.7839 (pm20) REVERT: C 813 PHE cc_start: 0.4925 (OUTLIER) cc_final: 0.4357 (t80) outliers start: 108 outliers final: 61 residues processed: 226 average time/residue: 0.5707 time to fit residues: 153.0007 Evaluate side-chains 204 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 131 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 770 LYS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 713 LYS Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain C residue 982 GLN Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 288 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 120 optimal weight: 6.9990 chunk 280 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 190 optimal weight: 0.0270 chunk 141 optimal weight: 0.0000 chunk 63 optimal weight: 3.9990 overall best weight: 0.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 741 GLN A 982 GLN B1081 HIS C 881 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.055276 restraints weight = 59088.641| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.40 r_work: 0.2657 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 27905 Z= 0.113 Angle : 0.634 9.671 38180 Z= 0.312 Chirality : 0.045 0.211 4516 Planarity : 0.004 0.041 4778 Dihedral : 7.563 90.568 5525 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.00 % Rotamer: Outliers : 2.94 % Allowed : 22.28 % Favored : 74.78 % 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 are not related in a simple way. whole: -1.09 (0.14), residues: 3303 helix: 0.64 (0.21), residues: 708 sheet: 0.42 (0.18), residues: 795 loop : -1.93 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 666 TYR 0.016 0.001 TYR B1047 PHE 0.024 0.001 PHE A1101 TRP 0.009 0.001 TRP B 425 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00246 (27779) covalent geometry : angle 0.60892 (37841) SS BOND : bond 0.00270 ( 39) SS BOND : angle 1.37229 ( 78) hydrogen bonds : bond 0.04287 ( 914) hydrogen bonds : angle 5.24814 ( 2577) link_ALPHA1-3 : bond 0.01107 ( 6) link_ALPHA1-3 : angle 1.91233 ( 18) link_ALPHA1-6 : bond 0.00869 ( 1) link_ALPHA1-6 : angle 1.32991 ( 3) link_BETA1-4 : bond 0.00594 ( 36) link_BETA1-4 : angle 1.99294 ( 108) link_NAG-ASN : bond 0.00262 ( 44) link_NAG-ASN : angle 2.24955 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 144 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.5208 (tp) REVERT: A 187 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.7875 (mm-40) REVERT: A 263 MET cc_start: 0.9224 (mmt) cc_final: 0.8997 (mmt) REVERT: A 816 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6359 (mm110) REVERT: A 846 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 968 GLU cc_start: 0.9092 (tp30) cc_final: 0.8753 (tp30) REVERT: A 1093 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7455 (tm-30) REVERT: A 1105 ASN cc_start: 0.9234 (p0) cc_final: 0.8801 (p0) REVERT: B 236 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6792 (mmt) REVERT: B 266 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: B 968 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8370 (tp30) REVERT: B 999 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8113 (tpm-80) REVERT: C 681 GLU cc_start: 0.8365 (mp0) cc_final: 0.7806 (pm20) REVERT: C 813 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.4395 (t80) outliers start: 85 outliers final: 48 residues processed: 208 average time/residue: 0.5896 time to fit residues: 144.9391 Evaluate side-chains 195 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 182 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 243 optimal weight: 0.3980 chunk 277 optimal weight: 0.4980 chunk 219 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 GLN B 982 GLN B1081 HIS C 171 ASN C 881 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.052602 restraints weight = 59741.610| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.39 r_work: 0.2593 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 27905 Z= 0.226 Angle : 0.707 9.690 38180 Z= 0.351 Chirality : 0.048 0.234 4516 Planarity : 0.004 0.042 4778 Dihedral : 7.580 88.465 5523 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 3.01 % Allowed : 22.25 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3303 helix: 0.55 (0.20), residues: 726 sheet: 0.40 (0.18), residues: 774 loop : -2.01 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 666 TYR 0.018 0.001 TYR B1047 PHE 0.026 0.002 PHE A1101 TRP 0.009 0.001 TRP A 425 HIS 0.004 0.001 HIS B 610 Details of bonding type rmsd covalent geometry : bond 0.00551 (27779) covalent geometry : angle 0.67704 (37841) SS BOND : bond 0.00458 ( 39) SS BOND : angle 1.94756 ( 78) hydrogen bonds : bond 0.05707 ( 914) hydrogen bonds : angle 5.37000 ( 2577) link_ALPHA1-3 : bond 0.00992 ( 6) link_ALPHA1-3 : angle 2.26047 ( 18) link_ALPHA1-6 : bond 0.01064 ( 1) link_ALPHA1-6 : angle 1.24382 ( 3) link_BETA1-4 : bond 0.00566 ( 36) link_BETA1-4 : angle 2.12583 ( 108) link_NAG-ASN : bond 0.00305 ( 44) link_NAG-ASN : angle 2.50975 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 136 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8588 (tm-30) REVERT: A 187 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.7886 (mm-40) REVERT: A 691 SER cc_start: 0.9554 (OUTLIER) cc_final: 0.9251 (t) REVERT: A 741 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8474 (tm-30) REVERT: A 770 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8621 (pmtt) REVERT: A 816 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6355 (mm110) REVERT: A 846 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8642 (p) REVERT: A 875 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8717 (pt0) REVERT: A 968 GLU cc_start: 0.9163 (tp30) cc_final: 0.8801 (tp30) REVERT: A 1093 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 1105 ASN cc_start: 0.9249 (p0) cc_final: 0.8816 (p0) REVERT: B 236 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6948 (mmt) REVERT: B 266 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8256 (tp30) REVERT: B 784 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8530 (pp30) REVERT: B 968 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8431 (tp30) REVERT: B 999 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8075 (tpm-80) REVERT: C 681 GLU cc_start: 0.8434 (mp0) cc_final: 0.7998 (pm20) REVERT: C 813 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.4440 (t80) REVERT: C 1102 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8096 (tm-30) outliers start: 87 outliers final: 53 residues processed: 204 average time/residue: 0.5581 time to fit residues: 134.5997 Evaluate side-chains 198 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 770 LYS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 713 LYS Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 203 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 280 optimal weight: 0.3980 chunk 295 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 GLN B 239 HIS B1081 HIS C 147 ASN C 881 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.054515 restraints weight = 59677.689| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.41 r_work: 0.2641 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27905 Z= 0.123 Angle : 0.646 13.743 38180 Z= 0.317 Chirality : 0.045 0.216 4516 Planarity : 0.004 0.041 4778 Dihedral : 7.192 88.492 5522 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 2.56 % Allowed : 22.80 % Favored : 74.65 % 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 are not related in a simple way. whole: -1.04 (0.14), residues: 3303 helix: 0.72 (0.20), residues: 726 sheet: 0.48 (0.18), residues: 774 loop : -1.92 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.016 0.001 TYR A1047 PHE 0.026 0.001 PHE A1101 TRP 0.010 0.001 TRP B 425 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00279 (27779) covalent geometry : angle 0.62231 (37841) SS BOND : bond 0.00275 ( 39) SS BOND : angle 1.36551 ( 78) hydrogen bonds : bond 0.04484 ( 914) hydrogen bonds : angle 5.26648 ( 2577) link_ALPHA1-3 : bond 0.01068 ( 6) link_ALPHA1-3 : angle 1.90125 ( 18) link_ALPHA1-6 : bond 0.00894 ( 1) link_ALPHA1-6 : angle 1.34910 ( 3) link_BETA1-4 : bond 0.00590 ( 36) link_BETA1-4 : angle 1.92587 ( 108) link_NAG-ASN : bond 0.00251 ( 44) link_NAG-ASN : angle 2.26615 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 142 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8541 (tm-30) REVERT: A 691 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9261 (t) REVERT: A 816 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6393 (mm110) REVERT: A 846 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8545 (p) REVERT: A 968 GLU cc_start: 0.9130 (tp30) cc_final: 0.8820 (tp30) REVERT: A 1093 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 1105 ASN cc_start: 0.9267 (p0) cc_final: 0.8821 (p0) REVERT: B 81 PHE cc_start: 0.3571 (OUTLIER) cc_final: 0.1992 (t80) REVERT: B 142 MET cc_start: 0.7758 (tpp) cc_final: 0.7142 (tpp) REVERT: B 143 PHE cc_start: 0.7954 (m-80) cc_final: 0.7648 (m-80) REVERT: B 266 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8212 (tp30) REVERT: B 968 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8395 (tp30) REVERT: B 999 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8090 (tpm-80) REVERT: C 187 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: C 681 GLU cc_start: 0.8413 (mp0) cc_final: 0.7973 (pm20) REVERT: C 813 PHE cc_start: 0.5181 (OUTLIER) cc_final: 0.4512 (t80) outliers start: 74 outliers final: 45 residues processed: 199 average time/residue: 0.6375 time to fit residues: 149.4980 Evaluate side-chains 189 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 97 optimal weight: 1.9990 chunk 240 optimal weight: 0.5980 chunk 229 optimal weight: 4.9990 chunk 293 optimal weight: 0.0060 chunk 22 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 982 GLN B1081 HIS C 147 ASN C 171 ASN C 881 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055505 restraints weight = 59462.313| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.40 r_work: 0.2666 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27905 Z= 0.112 Angle : 0.623 12.816 38180 Z= 0.306 Chirality : 0.044 0.225 4516 Planarity : 0.004 0.041 4778 Dihedral : 6.606 87.475 5519 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 1.97 % Allowed : 23.59 % Favored : 74.44 % 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 are not related in a simple way. whole: -0.85 (0.14), residues: 3303 helix: 0.94 (0.21), residues: 726 sheet: 0.64 (0.18), residues: 762 loop : -1.84 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 666 TYR 0.017 0.001 TYR B1047 PHE 0.026 0.001 PHE A1101 TRP 0.009 0.001 TRP A 425 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00250 (27779) covalent geometry : angle 0.60137 (37841) SS BOND : bond 0.00304 ( 39) SS BOND : angle 1.19166 ( 78) hydrogen bonds : bond 0.04077 ( 914) hydrogen bonds : angle 5.13088 ( 2577) link_ALPHA1-3 : bond 0.01050 ( 6) link_ALPHA1-3 : angle 1.56576 ( 18) link_ALPHA1-6 : bond 0.00770 ( 1) link_ALPHA1-6 : angle 1.38538 ( 3) link_BETA1-4 : bond 0.00581 ( 36) link_BETA1-4 : angle 1.84068 ( 108) link_NAG-ASN : bond 0.00225 ( 44) link_NAG-ASN : angle 2.12761 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 141 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8570 (tm-30) REVERT: A 691 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9258 (t) REVERT: A 816 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6357 (mm110) REVERT: A 846 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 968 GLU cc_start: 0.9121 (tp30) cc_final: 0.8830 (tp30) REVERT: A 1093 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 1105 ASN cc_start: 0.9274 (p0) cc_final: 0.8833 (p0) REVERT: B 81 PHE cc_start: 0.3680 (OUTLIER) cc_final: 0.2371 (t80) REVERT: B 142 MET cc_start: 0.7838 (tpp) cc_final: 0.6923 (tpp) REVERT: B 238 MET cc_start: 0.4411 (tpt) cc_final: 0.2432 (ppp) REVERT: B 266 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: B 968 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8385 (tp30) REVERT: B 999 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8127 (tpm-80) REVERT: C 187 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8449 (mt0) REVERT: C 681 GLU cc_start: 0.8391 (mp0) cc_final: 0.7942 (pm20) REVERT: C 813 PHE cc_start: 0.5285 (OUTLIER) cc_final: 0.4670 (t80) outliers start: 57 outliers final: 38 residues processed: 187 average time/residue: 0.6329 time to fit residues: 139.9029 Evaluate side-chains 181 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 813 PHE Chi-restraints excluded: chain C residue 881 GLN Chi-restraints excluded: chain C residue 935 ASN Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1101 PHE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 129 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 292 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 285 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 GLN C 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.055482 restraints weight = 58993.520| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.38 r_work: 0.2666 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 27905 Z= 0.165 Angle : 0.738 59.196 38180 Z= 0.392 Chirality : 0.048 1.199 4516 Planarity : 0.004 0.041 4778 Dihedral : 6.607 87.465 5518 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 1.69 % Allowed : 23.73 % Favored : 74.58 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -0.85 (0.14), residues: 3303 helix: 0.93 (0.21), residues: 726 sheet: 0.65 (0.18), residues: 762 loop : -1.83 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.017 0.001 TYR B1047 PHE 0.025 0.001 PHE A1101 TRP 0.008 0.001 TRP A 425 HIS 0.011 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00357 (27779) covalent geometry : angle 0.72058 (37841) SS BOND : bond 0.00258 ( 39) SS BOND : angle 1.17646 ( 78) hydrogen bonds : bond 0.04114 ( 914) hydrogen bonds : angle 5.13482 ( 2577) link_ALPHA1-3 : bond 0.01032 ( 6) link_ALPHA1-3 : angle 1.58126 ( 18) link_ALPHA1-6 : bond 0.00770 ( 1) link_ALPHA1-6 : angle 1.37903 ( 3) link_BETA1-4 : bond 0.00584 ( 36) link_BETA1-4 : angle 1.86870 ( 108) link_NAG-ASN : bond 0.00225 ( 44) link_NAG-ASN : angle 2.12732 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11926.87 seconds wall clock time: 203 minutes 28.69 seconds (12208.69 seconds total)