Starting phenix.real_space_refine on Sun May 25 21:21:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy2_60553/05_2025/8zy2_60553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy2_60553/05_2025/8zy2_60553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zy2_60553/05_2025/8zy2_60553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy2_60553/05_2025/8zy2_60553.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy2_60553/05_2025/8zy2_60553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy2_60553/05_2025/8zy2_60553.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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 120 5.16 5 C 17235 2.51 5 N 4416 2.21 5 O 5328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27099 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1051} Chain breaks: 4 Chain: "B" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1051} Chain breaks: 4 Chain: "C" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1051} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 17.90, per 1000 atoms: 0.66 Number of scatterers: 27099 At special positions: 0 Unit cell: (149.504, 150.672, 169.36, 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 120 16.00 O 5328 8.00 N 4416 7.00 C 17235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.02 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.02 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG 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-ASN " NAG A1201 " - " ASN A 331 " " NAG A1202 " - " ASN A 616 " " NAG A1203 " - " ASN A 705 " " NAG A1204 " - " ASN A1070 " " NAG A1205 " - " ASN A 165 " " NAG A1206 " - " ASN A 282 " " NAG A1207 " - " ASN A 343 " " NAG A1208 " - " ASN A 17 " " NAG A1209 " - " ASN A 370 " " NAG A1210 " - " ASN A 30 " " NAG A1211 " - " ASN A 61 " " NAG B1202 " - " ASN B 331 " " NAG B1203 " - " ASN B 616 " " NAG B1204 " - " ASN B 705 " " NAG B1205 " - " ASN B1070 " " NAG B1206 " - " ASN B 165 " " NAG B1207 " - " ASN B 282 " " NAG B1208 " - " ASN B 343 " " NAG B1209 " - " ASN B 17 " " NAG B1210 " - " ASN B 370 " " NAG B1211 " - " ASN B 30 " " NAG B1212 " - " ASN B 61 " " NAG C1202 " - " ASN C 331 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 705 " " NAG C1205 " - " ASN C1070 " " NAG C1206 " - " ASN C 165 " " NAG C1207 " - " ASN C 282 " " NAG C1208 " - " ASN C 343 " " NAG C1209 " - " ASN C 17 " " NAG C1210 " - " ASN C 370 " " NAG C1211 " - " ASN C 30 " " NAG C1212 " - " ASN C 61 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 713 " " NAG G 1 " - " ASN A 797 " " NAG H 1 " - " ASN A1094 " " NAG I 1 " - " ASN A1130 " " NAG J 1 " - " ASN A 149 " " NAG K 1 " - " ASN B 122 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 713 " " NAG N 1 " - " ASN B 797 " " NAG O 1 " - " ASN B1094 " " NAG P 1 " - " ASN B1130 " " NAG Q 1 " - " ASN B 149 " " NAG R 1 " - " ASN C 122 " " NAG S 1 " - " ASN C 234 " " NAG T 1 " - " ASN C 713 " " NAG U 1 " - " ASN C 797 " " NAG V 1 " - " ASN C1094 " " NAG W 1 " - " ASN C1130 " " NAG X 1 " - " ASN C 149 " Time building additional restraints: 7.24 Conformation dependent library (CDL) restraints added in 3.2 seconds 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 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: 73 helices and 53 sheets defined 24.4% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.781A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.627A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.661A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.726A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.604A pdb=" N LEU A 629 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 753 through 779 removed outlier: 3.890A pdb=" N THR A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 Processing helix chain 'A' and resid 844 through 852 Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.959A pdb=" N GLY A 887 " --> pdb=" O PHE A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 909 through 915 Processing helix chain 'A' and resid 915 through 935 Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.597A pdb=" N ILE A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1029 removed outlier: 3.585A pdb=" N GLU A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.501A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.575A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.016A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.530A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.514A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.602A pdb=" N LEU B 629 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 733 through 739 removed outlier: 3.548A pdb=" N CYS B 739 " --> pdb=" O THR B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 750 Processing helix chain 'B' and resid 753 through 779 removed outlier: 3.792A pdb=" N THR B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 821 Processing helix chain 'B' and resid 844 through 852 Processing helix chain 'B' and resid 862 through 880 removed outlier: 3.546A pdb=" N THR B 879 " --> pdb=" O ALA B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 909 through 915 Processing helix chain 'B' and resid 915 through 935 Processing helix chain 'B' and resid 941 through 961 Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.588A pdb=" N ILE B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1029 removed outlier: 3.581A pdb=" N GLU B1013 " --> pdb=" O ILE B1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.505A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.646A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.592A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.594A pdb=" N LEU C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.975A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 742 through 750 Processing helix chain 'C' and resid 753 through 779 removed outlier: 3.882A pdb=" N THR C 757 " --> pdb=" O GLY C 753 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 821 Processing helix chain 'C' and resid 845 through 852 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 893 through 906 Processing helix chain 'C' and resid 909 through 915 Processing helix chain 'C' and resid 915 through 935 Processing helix chain 'C' and resid 941 through 961 Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 removed outlier: 3.597A pdb=" N ILE C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1029 removed outlier: 3.594A pdb=" N GLU C1013 " --> pdb=" O ILE C1009 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.278A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 68 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.278A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.275A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 11.551A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.314A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.571A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.830A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.879A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.217A pdb=" N GLU A 654 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR A 692 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 697 through 699 removed outlier: 6.858A pdb=" N ALA A 697 " --> pdb=" O ILE C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.678A pdb=" N SER A 707 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A1072 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 709 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A1070 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A1068 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.678A pdb=" N SER A 707 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A1072 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 709 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A1070 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A1068 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.523A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AB9, first strand: chain 'A' and resid 1116 through 1121 removed outlier: 4.620A pdb=" N ALA A1083 " --> pdb=" O SER A1119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 29 removed outlier: 4.182A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 29 removed outlier: 4.182A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.540A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.436A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.318A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.571A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.944A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.812A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.197A pdb=" N GLU B 654 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N THR B 692 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.671A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.671A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B1072 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.484A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 783 through 785 Processing sheet with id=AD9, first strand: chain 'B' and resid 1116 through 1121 removed outlier: 4.616A pdb=" N ALA B1083 " --> pdb=" O SER B1119 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 29 removed outlier: 4.289A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 29 removed outlier: 4.289A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 210 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.548A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 11.538A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 152 through 156 removed outlier: 6.350A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.922A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.502A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.971A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.676A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 565 through 567 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.116A pdb=" N GLU C 654 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR C 692 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.647A pdb=" N SER C 707 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C1072 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA C 709 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C1070 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU C1068 " --> pdb=" O PRO C 711 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.647A pdb=" N SER C 707 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C1072 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA C 709 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C1070 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU C1068 " --> pdb=" O PRO C 711 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.491A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1116 through 1121 removed outlier: 4.640A pdb=" N ALA C1083 " --> pdb=" O SER C1119 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 2904 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.16 Time building geometry restraints manager: 8.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5237 1.33 - 1.45: 7215 1.45 - 1.58: 15094 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 27696 Sorted by residual: bond pdb=" C12 EIC C1201 " pdb=" C13 EIC C1201 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C12 EIC B1201 " pdb=" C13 EIC B1201 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C10 EIC B1201 " pdb=" C9 EIC B1201 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C12 EIC A1213 " pdb=" C13 EIC A1213 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C10 EIC C1201 " pdb=" C9 EIC C1201 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.31e+01 ... (remaining 27691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 37429 3.12 - 6.24: 213 6.24 - 9.36: 28 9.36 - 12.48: 4 12.48 - 15.60: 12 Bond angle restraints: 37686 Sorted by residual: angle pdb=" CA PHE B 562 " pdb=" CB PHE B 562 " pdb=" CG PHE B 562 " ideal model delta sigma weight residual 113.80 121.55 -7.75 1.00e+00 1.00e+00 6.00e+01 angle pdb=" CA PHE C 515 " pdb=" CB PHE C 515 " pdb=" CG PHE C 515 " ideal model delta sigma weight residual 113.80 121.10 -7.30 1.00e+00 1.00e+00 5.33e+01 angle pdb=" CA PHE A 515 " pdb=" CB PHE A 515 " pdb=" CG PHE A 515 " ideal model delta sigma weight residual 113.80 121.04 -7.24 1.00e+00 1.00e+00 5.25e+01 angle pdb=" C10 EIC C1201 " pdb=" C9 EIC C1201 " pdb=" C8 EIC C1201 " ideal model delta sigma weight residual 127.75 112.15 15.60 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C12 EIC A1213 " pdb=" C13 EIC A1213 " pdb=" C14 EIC A1213 " ideal model delta sigma weight residual 128.16 112.59 15.57 3.00e+00 1.11e-01 2.69e+01 ... (remaining 37681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.26: 16538 24.26 - 48.52: 764 48.52 - 72.78: 134 72.78 - 97.04: 31 97.04 - 121.30: 5 Dihedral angle restraints: 17472 sinusoidal: 7833 harmonic: 9639 Sorted by residual: dihedral pdb=" CB CYS C1078 " pdb=" SG CYS C1078 " pdb=" SG CYS C1122 " pdb=" CB CYS C1122 " ideal model delta sinusoidal sigma weight residual -86.00 -2.77 -83.23 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS A1078 " pdb=" SG CYS A1078 " pdb=" SG CYS A1122 " pdb=" CB CYS A1122 " ideal model delta sinusoidal sigma weight residual -86.00 -17.33 -68.67 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS B1078 " pdb=" SG CYS B1078 " pdb=" SG CYS B1122 " pdb=" CB CYS B1122 " ideal model delta sinusoidal sigma weight residual -86.00 -19.49 -66.51 1 1.00e+01 1.00e-02 5.77e+01 ... (remaining 17469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4179 0.100 - 0.200: 266 0.200 - 0.301: 17 0.301 - 0.401: 2 0.401 - 0.501: 3 Chirality restraints: 4467 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 3.98e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 4464 not shown) Planarity restraints: 4824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 EIC B1201 " 0.133 2.00e-02 2.50e+03 3.42e-01 1.17e+03 pdb=" C12 EIC B1201 " -0.436 2.00e-02 2.50e+03 pdb=" C13 EIC B1201 " 0.479 2.00e-02 2.50e+03 pdb=" C14 EIC B1201 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 EIC A1213 " -0.145 2.00e-02 2.50e+03 3.40e-01 1.16e+03 pdb=" C12 EIC A1213 " 0.445 2.00e-02 2.50e+03 pdb=" C13 EIC A1213 " -0.465 2.00e-02 2.50e+03 pdb=" C14 EIC A1213 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 EIC C1201 " 0.148 2.00e-02 2.50e+03 3.20e-01 1.02e+03 pdb=" C12 EIC C1201 " -0.418 2.00e-02 2.50e+03 pdb=" C13 EIC C1201 " 0.431 2.00e-02 2.50e+03 pdb=" C14 EIC C1201 " -0.161 2.00e-02 2.50e+03 ... (remaining 4821 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6970 2.80 - 3.33: 22488 3.33 - 3.85: 43101 3.85 - 4.38: 49555 4.38 - 4.90: 88171 Nonbonded interactions: 210285 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.310 3.040 nonbonded pdb=" ND2 ASN B 519 " pdb=" O PHE B 565 " model vdw 2.314 3.120 ... (remaining 210280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1136 or resid 1202 through 1211)) selection = (chain 'B' and (resid 14 through 1136 or resid 1202 through 1211)) selection = (chain 'C' and (resid 14 through 1136 or resid 1202 through 1211)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.680 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: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 66.200 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.200 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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 : 0.006 0.194 27814 Z= 0.290 Angle : 0.795 17.844 37997 Z= 0.388 Chirality : 0.053 0.501 4467 Planarity : 0.011 0.342 4770 Dihedral : 14.212 121.300 11145 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.17 % Allowed : 0.28 % Favored : 99.55 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3279 helix: 0.36 (0.19), residues: 720 sheet: 0.91 (0.19), residues: 705 loop : -1.51 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 152 HIS 0.003 0.001 HIS A 146 PHE 0.033 0.001 PHE A 515 TYR 0.024 0.001 TYR B 365 ARG 0.007 0.000 ARG C 843 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 54) link_NAG-ASN : angle 3.71411 ( 162) link_BETA1-4 : bond 0.01122 ( 21) link_BETA1-4 : angle 3.03757 ( 63) hydrogen bonds : bond 0.14805 ( 1030) hydrogen bonds : angle 6.11346 ( 2904) SS BOND : bond 0.00391 ( 43) SS BOND : angle 1.22966 ( 86) covalent geometry : bond 0.00570 (27696) covalent geometry : angle 0.74734 (37686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 3.020 Fit side-chains revert: symmetry clash REVERT: A 519 ASN cc_start: 0.7550 (m110) cc_final: 0.7128 (p0) REVERT: A 693 MET cc_start: 0.9219 (ptm) cc_final: 0.8931 (ptm) REVERT: C 515 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.8412 (m-80) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 1.4073 time to fit residues: 109.8481 Evaluate side-chains 43 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 157 optimal weight: 0.0980 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 10.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.037152 restraints weight = 93820.216| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 3.61 r_work: 0.2437 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27814 Z= 0.201 Angle : 0.590 10.371 37997 Z= 0.292 Chirality : 0.046 0.366 4467 Planarity : 0.004 0.066 4770 Dihedral : 9.274 114.536 5264 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.21 % Allowed : 3.95 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3279 helix: 1.46 (0.21), residues: 696 sheet: 0.75 (0.19), residues: 729 loop : -1.29 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.003 0.001 HIS B1054 PHE 0.031 0.001 PHE A 562 TYR 0.019 0.001 TYR B 365 ARG 0.006 0.000 ARG A 843 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 54) link_NAG-ASN : angle 2.92756 ( 162) link_BETA1-4 : bond 0.00223 ( 21) link_BETA1-4 : angle 1.74295 ( 63) hydrogen bonds : bond 0.05189 ( 1030) hydrogen bonds : angle 5.16769 ( 2904) SS BOND : bond 0.00403 ( 43) SS BOND : angle 1.25694 ( 86) covalent geometry : bond 0.00469 (27696) covalent geometry : angle 0.55250 (37686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 ASN cc_start: 0.8078 (m110) cc_final: 0.7372 (p0) REVERT: A 693 MET cc_start: 0.9343 (ptm) cc_final: 0.8978 (ptm) REVERT: B 1025 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.9205 (tpp) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 1.2902 time to fit residues: 71.5870 Evaluate side-chains 46 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 1025 MET Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 179 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 219 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.037371 restraints weight = 92967.216| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 3.65 r_work: 0.2441 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27814 Z= 0.144 Angle : 0.538 10.090 37997 Z= 0.267 Chirality : 0.045 0.361 4467 Planarity : 0.003 0.043 4770 Dihedral : 8.602 114.298 5260 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.62 % Allowed : 5.44 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3279 helix: 1.74 (0.21), residues: 693 sheet: 0.77 (0.19), residues: 750 loop : -1.21 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.002 0.001 HIS C 69 PHE 0.030 0.001 PHE A 562 TYR 0.019 0.001 TYR C 365 ARG 0.005 0.000 ARG A 843 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 54) link_NAG-ASN : angle 2.77373 ( 162) link_BETA1-4 : bond 0.00271 ( 21) link_BETA1-4 : angle 1.81868 ( 63) hydrogen bonds : bond 0.04645 ( 1030) hydrogen bonds : angle 4.92122 ( 2904) SS BOND : bond 0.00316 ( 43) SS BOND : angle 1.00485 ( 86) covalent geometry : bond 0.00331 (27696) covalent geometry : angle 0.50070 (37686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASN cc_start: 0.8188 (m110) cc_final: 0.7528 (p0) REVERT: A 693 MET cc_start: 0.9317 (ptm) cc_final: 0.8967 (ptm) REVERT: A 865 MET cc_start: 0.9168 (mtt) cc_final: 0.8939 (mtt) REVERT: B 1025 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9159 (tpp) outliers start: 18 outliers final: 9 residues processed: 60 average time/residue: 1.3223 time to fit residues: 97.2825 Evaluate side-chains 53 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1025 MET Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 930 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 280 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 86 optimal weight: 0.8980 chunk 302 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 286 optimal weight: 0.5980 chunk 328 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.038260 restraints weight = 93428.545| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 3.65 r_work: 0.2478 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27814 Z= 0.094 Angle : 0.519 10.443 37997 Z= 0.255 Chirality : 0.044 0.365 4467 Planarity : 0.003 0.056 4770 Dihedral : 8.208 114.635 5258 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.73 % Allowed : 6.69 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3279 helix: 1.85 (0.21), residues: 696 sheet: 0.89 (0.20), residues: 720 loop : -1.11 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.006 0.000 HIS A 146 PHE 0.028 0.001 PHE A 562 TYR 0.019 0.001 TYR C 365 ARG 0.009 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 54) link_NAG-ASN : angle 2.64942 ( 162) link_BETA1-4 : bond 0.00317 ( 21) link_BETA1-4 : angle 1.77919 ( 63) hydrogen bonds : bond 0.03982 ( 1030) hydrogen bonds : angle 4.70410 ( 2904) SS BOND : bond 0.00437 ( 43) SS BOND : angle 0.99390 ( 86) covalent geometry : bond 0.00201 (27696) covalent geometry : angle 0.48396 (37686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7763 (tm) REVERT: A 519 ASN cc_start: 0.8127 (m110) cc_final: 0.7458 (p0) REVERT: A 693 MET cc_start: 0.9321 (ptm) cc_final: 0.8928 (ptm) REVERT: A 865 MET cc_start: 0.9153 (mtt) cc_final: 0.8901 (mtt) REVERT: C 1025 MET cc_start: 0.9371 (tpp) cc_final: 0.9100 (tpp) outliers start: 21 outliers final: 8 residues processed: 63 average time/residue: 1.2351 time to fit residues: 96.4462 Evaluate side-chains 53 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 984 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 46 optimal weight: 0.0370 chunk 216 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 305 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 309 optimal weight: 3.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 832 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.037947 restraints weight = 93186.009| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 3.65 r_work: 0.2462 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27814 Z= 0.114 Angle : 0.519 10.385 37997 Z= 0.255 Chirality : 0.044 0.364 4467 Planarity : 0.003 0.038 4770 Dihedral : 7.959 115.172 5256 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.07 % Allowed : 7.28 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3279 helix: 1.93 (0.21), residues: 693 sheet: 0.86 (0.19), residues: 738 loop : -1.06 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 152 HIS 0.002 0.000 HIS C 69 PHE 0.031 0.001 PHE A 562 TYR 0.017 0.001 TYR C1063 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 54) link_NAG-ASN : angle 2.59871 ( 162) link_BETA1-4 : bond 0.00270 ( 21) link_BETA1-4 : angle 1.76282 ( 63) hydrogen bonds : bond 0.04102 ( 1030) hydrogen bonds : angle 4.65074 ( 2904) SS BOND : bond 0.00303 ( 43) SS BOND : angle 1.06420 ( 86) covalent geometry : bond 0.00260 (27696) covalent geometry : angle 0.48479 (37686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 45 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7704 (tm) REVERT: A 519 ASN cc_start: 0.8163 (m110) cc_final: 0.7536 (p0) REVERT: A 693 MET cc_start: 0.9309 (ptm) cc_final: 0.8937 (ptm) REVERT: B 896 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9133 (mtm) outliers start: 31 outliers final: 16 residues processed: 72 average time/residue: 1.0968 time to fit residues: 99.7489 Evaluate side-chains 61 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 984 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 140 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 GLN B 334 ASN B 388 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.050911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.035225 restraints weight = 95078.062| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 3.59 r_work: 0.2377 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 27814 Z= 0.358 Angle : 0.672 10.209 37997 Z= 0.334 Chirality : 0.049 0.353 4467 Planarity : 0.004 0.039 4770 Dihedral : 8.429 115.821 5256 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.04 % Allowed : 7.90 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3279 helix: 1.38 (0.20), residues: 732 sheet: 0.62 (0.19), residues: 771 loop : -1.31 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.006 0.001 HIS A 207 PHE 0.037 0.002 PHE A 562 TYR 0.026 0.002 TYR B 266 ARG 0.005 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 54) link_NAG-ASN : angle 2.85894 ( 162) link_BETA1-4 : bond 0.00158 ( 21) link_BETA1-4 : angle 1.78580 ( 63) hydrogen bonds : bond 0.06122 ( 1030) hydrogen bonds : angle 5.18586 ( 2904) SS BOND : bond 0.00604 ( 43) SS BOND : angle 1.57326 ( 86) covalent geometry : bond 0.00850 (27696) covalent geometry : angle 0.63999 (37686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8011 (tm) REVERT: A 519 ASN cc_start: 0.8244 (m110) cc_final: 0.7755 (p0) REVERT: A 693 MET cc_start: 0.9376 (ptm) cc_final: 0.9049 (ptm) outliers start: 30 outliers final: 22 residues processed: 69 average time/residue: 0.9862 time to fit residues: 86.6433 Evaluate side-chains 66 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 984 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 235 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 326 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.052787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.037193 restraints weight = 93386.283| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 3.64 r_work: 0.2435 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27814 Z= 0.106 Angle : 0.539 11.558 37997 Z= 0.264 Chirality : 0.045 0.364 4467 Planarity : 0.003 0.040 4770 Dihedral : 7.990 114.210 5256 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.90 % Allowed : 8.00 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3279 helix: 1.75 (0.21), residues: 711 sheet: 0.71 (0.19), residues: 747 loop : -1.13 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 152 HIS 0.002 0.000 HIS A 146 PHE 0.032 0.001 PHE A 562 TYR 0.021 0.001 TYR C 365 ARG 0.002 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 54) link_NAG-ASN : angle 2.69666 ( 162) link_BETA1-4 : bond 0.00344 ( 21) link_BETA1-4 : angle 1.85087 ( 63) hydrogen bonds : bond 0.04447 ( 1030) hydrogen bonds : angle 4.76908 ( 2904) SS BOND : bond 0.00320 ( 43) SS BOND : angle 1.04180 ( 86) covalent geometry : bond 0.00233 (27696) covalent geometry : angle 0.50309 (37686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7941 (tm) REVERT: A 519 ASN cc_start: 0.8199 (m110) cc_final: 0.7641 (p0) REVERT: A 693 MET cc_start: 0.9358 (ptm) cc_final: 0.9011 (ptm) REVERT: A 865 MET cc_start: 0.9187 (mtt) cc_final: 0.8773 (mtt) outliers start: 26 outliers final: 22 residues processed: 68 average time/residue: 1.0259 time to fit residues: 89.2194 Evaluate side-chains 66 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 984 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 258 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 116 optimal weight: 0.0030 chunk 324 optimal weight: 0.9980 chunk 55 optimal weight: 0.0040 chunk 149 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 175 optimal weight: 5.9990 chunk 313 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.038194 restraints weight = 93166.443| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 3.65 r_work: 0.2471 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27814 Z= 0.089 Angle : 0.512 11.784 37997 Z= 0.249 Chirality : 0.044 0.371 4467 Planarity : 0.003 0.038 4770 Dihedral : 7.663 115.722 5256 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.90 % Allowed : 8.39 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3279 helix: 1.84 (0.21), residues: 714 sheet: 0.86 (0.19), residues: 735 loop : -1.02 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 152 HIS 0.002 0.000 HIS C 69 PHE 0.029 0.001 PHE A 562 TYR 0.020 0.001 TYR C 365 ARG 0.001 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 54) link_NAG-ASN : angle 2.54694 ( 162) link_BETA1-4 : bond 0.00332 ( 21) link_BETA1-4 : angle 1.82460 ( 63) hydrogen bonds : bond 0.03769 ( 1030) hydrogen bonds : angle 4.54725 ( 2904) SS BOND : bond 0.00257 ( 43) SS BOND : angle 0.85058 ( 86) covalent geometry : bond 0.00189 (27696) covalent geometry : angle 0.47879 (37686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7954 (tm) REVERT: A 519 ASN cc_start: 0.8178 (m110) cc_final: 0.7780 (p0) REVERT: A 693 MET cc_start: 0.9382 (ptm) cc_final: 0.9008 (ptm) REVERT: A 865 MET cc_start: 0.9180 (mtt) cc_final: 0.8804 (mtt) outliers start: 26 outliers final: 22 residues processed: 70 average time/residue: 0.9699 time to fit residues: 87.1632 Evaluate side-chains 69 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 984 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 50 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.036024 restraints weight = 94546.537| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 3.60 r_work: 0.2401 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 27814 Z= 0.254 Angle : 0.603 11.281 37997 Z= 0.297 Chirality : 0.046 0.356 4467 Planarity : 0.003 0.039 4770 Dihedral : 7.971 116.243 5256 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.97 % Allowed : 8.39 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3279 helix: 1.68 (0.21), residues: 714 sheet: 0.67 (0.19), residues: 771 loop : -1.13 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.004 0.001 HIS B1054 PHE 0.032 0.001 PHE A 562 TYR 0.019 0.001 TYR B 266 ARG 0.004 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 54) link_NAG-ASN : angle 2.70356 ( 162) link_BETA1-4 : bond 0.00123 ( 21) link_BETA1-4 : angle 1.79847 ( 63) hydrogen bonds : bond 0.05337 ( 1030) hydrogen bonds : angle 4.92407 ( 2904) SS BOND : bond 0.00481 ( 43) SS BOND : angle 1.29752 ( 86) covalent geometry : bond 0.00597 (27696) covalent geometry : angle 0.57135 (37686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 45 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8082 (tm) REVERT: A 519 ASN cc_start: 0.8280 (m110) cc_final: 0.7875 (p0) REVERT: A 693 MET cc_start: 0.9356 (ptm) cc_final: 0.9020 (ptm) outliers start: 28 outliers final: 25 residues processed: 70 average time/residue: 1.0031 time to fit residues: 89.8435 Evaluate side-chains 71 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 984 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 234 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 295 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: ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.036779 restraints weight = 93833.730| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 3.65 r_work: 0.2423 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27814 Z= 0.146 Angle : 0.552 12.168 37997 Z= 0.269 Chirality : 0.045 0.361 4467 Planarity : 0.003 0.038 4770 Dihedral : 7.821 115.152 5256 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.94 % Allowed : 8.49 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3279 helix: 1.75 (0.21), residues: 714 sheet: 0.66 (0.19), residues: 768 loop : -1.07 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.002 0.001 HIS B 146 PHE 0.030 0.001 PHE A 562 TYR 0.022 0.001 TYR C 365 ARG 0.002 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 54) link_NAG-ASN : angle 2.65023 ( 162) link_BETA1-4 : bond 0.00248 ( 21) link_BETA1-4 : angle 1.83212 ( 63) hydrogen bonds : bond 0.04616 ( 1030) hydrogen bonds : angle 4.76751 ( 2904) SS BOND : bond 0.00356 ( 43) SS BOND : angle 1.04256 ( 86) covalent geometry : bond 0.00338 (27696) covalent geometry : angle 0.51808 (37686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6558 Ramachandran restraints generated. 3279 Oldfield, 0 Emsley, 3279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8024 (tm) REVERT: A 519 ASN cc_start: 0.8265 (m110) cc_final: 0.7820 (p0) REVERT: A 693 MET cc_start: 0.9342 (ptm) cc_final: 0.8990 (ptm) outliers start: 27 outliers final: 26 residues processed: 74 average time/residue: 0.9771 time to fit residues: 92.8872 Evaluate side-chains 74 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 984 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 109 optimal weight: 0.0570 chunk 157 optimal weight: 0.0570 chunk 45 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.038345 restraints weight = 92965.836| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 3.63 r_work: 0.2472 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27814 Z= 0.089 Angle : 0.519 12.532 37997 Z= 0.250 Chirality : 0.044 0.368 4467 Planarity : 0.003 0.037 4770 Dihedral : 7.484 115.109 5256 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.94 % Allowed : 8.56 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3279 helix: 1.87 (0.21), residues: 714 sheet: 0.83 (0.19), residues: 738 loop : -1.00 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 152 HIS 0.002 0.000 HIS B 245 PHE 0.032 0.001 PHE A 562 TYR 0.021 0.001 TYR C 365 ARG 0.002 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 54) link_NAG-ASN : angle 2.54834 ( 162) link_BETA1-4 : bond 0.00366 ( 21) link_BETA1-4 : angle 1.85869 ( 63) hydrogen bonds : bond 0.03675 ( 1030) hydrogen bonds : angle 4.52116 ( 2904) SS BOND : bond 0.00261 ( 43) SS BOND : angle 0.77566 ( 86) covalent geometry : bond 0.00191 (27696) covalent geometry : angle 0.48639 (37686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11154.48 seconds wall clock time: 195 minutes 26.40 seconds (11726.40 seconds total)