Starting phenix.real_space_refine on Mon Aug 25 10:33:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy2_60553/08_2025/8zy2_60553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy2_60553/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zy2_60553/08_2025/8zy2_60553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy2_60553/08_2025/8zy2_60553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zy2_60553/08_2025/8zy2_60553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy2_60553/08_2025/8zy2_60553.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.15, per 1000 atoms: 0.23 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: 2.19 Conformation dependent library (CDL) restraints added in 891.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.29 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: 6.08 Time building geometry restraints manager: 2.93 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: 0.02 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.830 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- 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 : 3.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (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 ARG 0.007 0.000 ARG C 843 TYR 0.024 0.001 TYR B 365 PHE 0.033 0.001 PHE A 515 TRP 0.011 0.001 TRP C 152 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00570 (27696) covalent geometry : angle 0.74734 (37686) SS BOND : bond 0.00391 ( 43) SS BOND : angle 1.22966 ( 86) hydrogen bonds : bond 0.14805 ( 1030) hydrogen bonds : angle 6.11346 ( 2904) link_BETA1-4 : bond 0.01122 ( 21) link_BETA1-4 : angle 3.03757 ( 63) link_NAG-ASN : bond 0.00612 ( 54) link_NAG-ASN : angle 3.71411 ( 162) *********************** 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 : 1.035 Fit side-chains REVERT: A 519 ASN cc_start: 0.7550 (m110) cc_final: 0.7127 (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: 0.5663 time to fit residues: 43.4148 Evaluate side-chains 42 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** 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 = 0.3076 r_free = 0.3076 target = 0.053024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.037361 restraints weight = 93894.688| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 3.65 r_work: 0.2451 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27814 Z= 0.184 Angle : 0.602 20.710 37997 Z= 0.293 Chirality : 0.048 0.967 4467 Planarity : 0.004 0.068 4770 Dihedral : 9.355 114.304 5264 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.21 % Allowed : 4.09 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.15), residues: 3279 helix: 1.52 (0.21), residues: 693 sheet: 0.85 (0.20), residues: 699 loop : -1.28 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 843 TYR 0.019 0.001 TYR B 365 PHE 0.031 0.001 PHE A 562 TRP 0.012 0.001 TRP A 152 HIS 0.003 0.001 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00424 (27696) covalent geometry : angle 0.55259 (37686) SS BOND : bond 0.00368 ( 43) SS BOND : angle 1.21743 ( 86) hydrogen bonds : bond 0.04936 ( 1030) hydrogen bonds : angle 5.12145 ( 2904) link_BETA1-4 : bond 0.00293 ( 21) link_BETA1-4 : angle 1.72928 ( 63) link_NAG-ASN : bond 0.00592 ( 54) link_NAG-ASN : angle 3.47183 ( 162) *********************** 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 48 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 ASN cc_start: 0.8101 (m110) cc_final: 0.7396 (p0) REVERT: A 693 MET cc_start: 0.9334 (ptm) cc_final: 0.8967 (ptm) REVERT: B 1025 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.9154 (tpp) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.5998 time to fit residues: 32.9852 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 : 0.947 ------------------------------------------------------------------------------- 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 201 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN B 564 GLN C 14 GLN C 832 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.051608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.035954 restraints weight = 94683.143| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 3.60 r_work: 0.2399 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 27814 Z= 0.255 Angle : 0.616 13.257 37997 Z= 0.306 Chirality : 0.048 0.598 4467 Planarity : 0.004 0.042 4770 Dihedral : 8.879 114.507 5260 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.76 % Allowed : 5.99 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3279 helix: 1.35 (0.21), residues: 729 sheet: 0.70 (0.19), residues: 750 loop : -1.37 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 214 TYR 0.021 0.001 TYR B 266 PHE 0.034 0.002 PHE A 562 TRP 0.010 0.001 TRP A 152 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00604 (27696) covalent geometry : angle 0.57613 (37686) SS BOND : bond 0.00455 ( 43) SS BOND : angle 1.23433 ( 86) hydrogen bonds : bond 0.05654 ( 1030) hydrogen bonds : angle 5.15613 ( 2904) link_BETA1-4 : bond 0.00146 ( 21) link_BETA1-4 : angle 1.81521 ( 63) link_NAG-ASN : bond 0.00457 ( 54) link_NAG-ASN : angle 3.09550 ( 162) *********************** 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: 22 poor density : 42 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASN cc_start: 0.8248 (m110) cc_final: 0.7599 (p0) REVERT: A 693 MET cc_start: 0.9318 (ptm) cc_final: 0.8960 (ptm) REVERT: B 1025 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.8679 (tpp) REVERT: C 1025 MET cc_start: 0.9408 (tpp) cc_final: 0.9062 (tpp) outliers start: 22 outliers final: 10 residues processed: 60 average time/residue: 0.5299 time to fit residues: 38.6447 Evaluate side-chains 52 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 17 ASN 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 43 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 chunk 255 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 82 optimal weight: 0.0870 chunk 16 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.037394 restraints weight = 93132.109| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.60 r_work: 0.2447 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27814 Z= 0.114 Angle : 0.546 11.936 37997 Z= 0.267 Chirality : 0.045 0.521 4467 Planarity : 0.003 0.043 4770 Dihedral : 8.369 113.811 5258 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.87 % Allowed : 6.93 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 3279 helix: 1.67 (0.21), residues: 711 sheet: 0.74 (0.19), residues: 765 loop : -1.20 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.020 0.001 TYR C 365 PHE 0.029 0.001 PHE A 562 TRP 0.013 0.001 TRP A 152 HIS 0.006 0.000 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00252 (27696) covalent geometry : angle 0.50561 (37686) SS BOND : bond 0.00478 ( 43) SS BOND : angle 1.11353 ( 86) hydrogen bonds : bond 0.04403 ( 1030) hydrogen bonds : angle 4.82111 ( 2904) link_BETA1-4 : bond 0.00310 ( 21) link_BETA1-4 : angle 1.81132 ( 63) link_NAG-ASN : bond 0.00477 ( 54) link_NAG-ASN : angle 2.90510 ( 162) *********************** 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 70 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASN cc_start: 0.8183 (m110) cc_final: 0.7600 (p0) REVERT: A 693 MET cc_start: 0.9284 (ptm) cc_final: 0.8944 (ptm) REVERT: A 865 MET cc_start: 0.9218 (mtt) cc_final: 0.8835 (mtt) REVERT: C 1025 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9078 (tpp) outliers start: 25 outliers final: 13 residues processed: 66 average time/residue: 0.4848 time to fit residues: 39.3879 Evaluate side-chains 57 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 C residue 17 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 1025 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 47 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 145 optimal weight: 0.0370 chunk 329 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 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 = 0.3045 r_free = 0.3045 target = 0.051878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.036304 restraints weight = 94109.720| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 3.59 r_work: 0.2410 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27814 Z= 0.217 Angle : 0.586 11.122 37997 Z= 0.289 Chirality : 0.046 0.511 4467 Planarity : 0.003 0.040 4770 Dihedral : 8.332 114.395 5256 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.18 % Allowed : 7.66 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 3279 helix: 1.63 (0.21), residues: 711 sheet: 0.67 (0.19), residues: 771 loop : -1.23 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 214 TYR 0.020 0.001 TYR C 365 PHE 0.031 0.001 PHE A 562 TRP 0.016 0.001 TRP A 152 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00513 (27696) covalent geometry : angle 0.54904 (37686) SS BOND : bond 0.00447 ( 43) SS BOND : angle 1.30655 ( 86) hydrogen bonds : bond 0.05149 ( 1030) hydrogen bonds : angle 4.95544 ( 2904) link_BETA1-4 : bond 0.00154 ( 21) link_BETA1-4 : angle 1.78895 ( 63) link_NAG-ASN : bond 0.00414 ( 54) link_NAG-ASN : angle 2.89537 ( 162) *********************** 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 77 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 43 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8040 (tm) REVERT: A 519 ASN cc_start: 0.8222 (m110) cc_final: 0.7730 (p0) REVERT: A 693 MET cc_start: 0.9299 (ptm) cc_final: 0.8990 (ptm) REVERT: A 865 MET cc_start: 0.9210 (mtt) cc_final: 0.8885 (mtt) REVERT: C 1025 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.9045 (tpp) outliers start: 34 outliers final: 25 residues processed: 72 average time/residue: 0.4240 time to fit residues: 38.3372 Evaluate side-chains 70 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 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 898 MET Chi-restraints excluded: chain C residue 17 ASN 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 984 GLU Chi-restraints excluded: chain C residue 1025 MET Chi-restraints excluded: chain C residue 1132 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 188 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 0.0670 chunk 287 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.037132 restraints weight = 93479.515| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 3.63 r_work: 0.2434 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27814 Z= 0.126 Angle : 0.539 10.929 37997 Z= 0.264 Chirality : 0.045 0.471 4467 Planarity : 0.003 0.040 4770 Dihedral : 8.070 113.427 5256 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.11 % Allowed : 8.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 3279 helix: 1.72 (0.21), residues: 711 sheet: 0.70 (0.19), residues: 765 loop : -1.14 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.021 0.001 TYR C 365 PHE 0.029 0.001 PHE A 562 TRP 0.013 0.001 TRP A 152 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00287 (27696) covalent geometry : angle 0.50052 (37686) SS BOND : bond 0.00356 ( 43) SS BOND : angle 1.08187 ( 86) hydrogen bonds : bond 0.04428 ( 1030) hydrogen bonds : angle 4.76566 ( 2904) link_BETA1-4 : bond 0.00284 ( 21) link_BETA1-4 : angle 1.83037 ( 63) link_NAG-ASN : bond 0.00441 ( 54) link_NAG-ASN : angle 2.81397 ( 162) *********************** 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 77 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 45 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8003 (tm) REVERT: A 519 ASN cc_start: 0.8210 (m110) cc_final: 0.7644 (p0) REVERT: A 693 MET cc_start: 0.9269 (ptm) cc_final: 0.8952 (ptm) REVERT: A 865 MET cc_start: 0.9161 (mtt) cc_final: 0.8807 (mtt) REVERT: C 1025 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9037 (tpp) outliers start: 32 outliers final: 25 residues processed: 72 average time/residue: 0.4430 time to fit residues: 40.4935 Evaluate side-chains 70 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 562 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 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 898 MET Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 17 ASN 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 Chi-restraints excluded: chain C residue 1025 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 208 optimal weight: 2.9990 chunk 300 optimal weight: 0.0050 chunk 156 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.038002 restraints weight = 93032.688| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 3.63 r_work: 0.2462 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27814 Z= 0.100 Angle : 0.519 11.272 37997 Z= 0.252 Chirality : 0.045 0.435 4467 Planarity : 0.003 0.038 4770 Dihedral : 7.758 113.894 5256 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.32 % Allowed : 8.25 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 3279 helix: 1.80 (0.21), residues: 714 sheet: 0.83 (0.20), residues: 639 loop : -1.09 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.021 0.001 TYR C 365 PHE 0.026 0.001 PHE A 562 TRP 0.012 0.001 TRP B 152 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00221 (27696) covalent geometry : angle 0.48256 (37686) SS BOND : bond 0.00274 ( 43) SS BOND : angle 0.88360 ( 86) hydrogen bonds : bond 0.03886 ( 1030) hydrogen bonds : angle 4.58788 ( 2904) link_BETA1-4 : bond 0.00310 ( 21) link_BETA1-4 : angle 1.83621 ( 63) link_NAG-ASN : bond 0.00453 ( 54) link_NAG-ASN : angle 2.70383 ( 162) *********************** 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 82 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 44 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8044 (tm) REVERT: A 519 ASN cc_start: 0.8192 (m110) cc_final: 0.7647 (p0) REVERT: A 693 MET cc_start: 0.9264 (ptm) cc_final: 0.8927 (ptm) REVERT: A 865 MET cc_start: 0.9178 (mtt) cc_final: 0.8781 (mtt) REVERT: C 1025 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9057 (tpp) outliers start: 38 outliers final: 27 residues processed: 78 average time/residue: 0.4133 time to fit residues: 40.4030 Evaluate side-chains 72 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 62 VAL 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 898 MET Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 17 ASN 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 Chi-restraints excluded: chain C residue 1025 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 301 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 286 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.037444 restraints weight = 93823.755| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 3.65 r_work: 0.2445 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27814 Z= 0.129 Angle : 0.534 11.226 37997 Z= 0.259 Chirality : 0.045 0.436 4467 Planarity : 0.003 0.038 4770 Dihedral : 7.747 113.840 5256 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.14 % Allowed : 8.49 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 3279 helix: 1.83 (0.21), residues: 708 sheet: 0.81 (0.20), residues: 636 loop : -1.10 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.020 0.001 TYR C 365 PHE 0.026 0.001 PHE A 562 TRP 0.011 0.001 TRP A 152 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00300 (27696) covalent geometry : angle 0.49828 (37686) SS BOND : bond 0.00315 ( 43) SS BOND : angle 0.94276 ( 86) hydrogen bonds : bond 0.04201 ( 1030) hydrogen bonds : angle 4.63380 ( 2904) link_BETA1-4 : bond 0.00250 ( 21) link_BETA1-4 : angle 1.80562 ( 63) link_NAG-ASN : bond 0.00416 ( 54) link_NAG-ASN : angle 2.69819 ( 162) *********************** 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 78 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 45 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8066 (tm) REVERT: A 519 ASN cc_start: 0.8243 (m110) cc_final: 0.7734 (p0) REVERT: A 693 MET cc_start: 0.9271 (ptm) cc_final: 0.8941 (ptm) REVERT: A 865 MET cc_start: 0.9183 (mtt) cc_final: 0.8826 (mtt) REVERT: B 66 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.6910 (p90) REVERT: C 1025 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9052 (tpp) outliers start: 33 outliers final: 28 residues processed: 74 average time/residue: 0.4341 time to fit residues: 41.0122 Evaluate side-chains 75 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 44 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 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 62 VAL Chi-restraints excluded: chain B residue 66 HIS 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 898 MET Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 62 VAL 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 Chi-restraints excluded: chain C residue 1025 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 160 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 150 optimal weight: 0.1980 chunk 217 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 292 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.053277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.037747 restraints weight = 93591.824| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 3.64 r_work: 0.2453 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1349 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= 0.112 Angle : 0.526 11.643 37997 Z= 0.255 Chirality : 0.045 0.427 4467 Planarity : 0.003 0.037 4770 Dihedral : 7.650 114.163 5256 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.25 % Allowed : 8.52 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.15), residues: 3279 helix: 1.79 (0.21), residues: 717 sheet: 0.81 (0.20), residues: 636 loop : -1.06 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.020 0.001 TYR C 365 PHE 0.026 0.001 PHE A 562 TRP 0.011 0.001 TRP A 152 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00254 (27696) covalent geometry : angle 0.49049 (37686) SS BOND : bond 0.00291 ( 43) SS BOND : angle 0.88777 ( 86) hydrogen bonds : bond 0.04046 ( 1030) hydrogen bonds : angle 4.59094 ( 2904) link_BETA1-4 : bond 0.00290 ( 21) link_BETA1-4 : angle 1.81936 ( 63) link_NAG-ASN : bond 0.00436 ( 54) link_NAG-ASN : angle 2.68025 ( 162) *********************** 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 80 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 44 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8074 (tm) REVERT: A 519 ASN cc_start: 0.8238 (m110) cc_final: 0.7764 (p0) REVERT: A 693 MET cc_start: 0.9342 (ptm) cc_final: 0.8999 (ptm) REVERT: A 865 MET cc_start: 0.9168 (mtt) cc_final: 0.8809 (mtt) REVERT: B 66 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.6891 (p90) REVERT: C 1025 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9074 (tpp) outliers start: 36 outliers final: 28 residues processed: 76 average time/residue: 0.4247 time to fit residues: 41.3076 Evaluate side-chains 75 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 44 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 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 62 VAL Chi-restraints excluded: chain B residue 66 HIS 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 898 MET Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 62 VAL 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 Chi-restraints excluded: chain C residue 1025 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 215 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 320 optimal weight: 3.9990 chunk 251 optimal weight: 0.0670 chunk 140 optimal weight: 6.9990 chunk 324 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.038291 restraints weight = 93644.360| |-----------------------------------------------------------------------------| r_work (start): 0.2615 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: 0.8674 moved from start: 0.1369 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= 0.092 Angle : 0.518 12.291 37997 Z= 0.250 Chirality : 0.044 0.415 4467 Planarity : 0.003 0.036 4770 Dihedral : 7.517 114.345 5256 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.11 % Allowed : 8.70 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 3279 helix: 1.83 (0.21), residues: 717 sheet: 0.77 (0.20), residues: 642 loop : -1.01 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.020 0.001 TYR C 365 PHE 0.025 0.001 PHE A 562 TRP 0.011 0.001 TRP A 152 HIS 0.002 0.000 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00201 (27696) covalent geometry : angle 0.48303 (37686) SS BOND : bond 0.00255 ( 43) SS BOND : angle 0.94778 ( 86) hydrogen bonds : bond 0.03735 ( 1030) hydrogen bonds : angle 4.51122 ( 2904) link_BETA1-4 : bond 0.00326 ( 21) link_BETA1-4 : angle 1.81364 ( 63) link_NAG-ASN : bond 0.00452 ( 54) link_NAG-ASN : angle 2.63465 ( 162) ********************** 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 77 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 45 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8071 (tm) REVERT: A 519 ASN cc_start: 0.8221 (m110) cc_final: 0.7755 (p0) REVERT: A 693 MET cc_start: 0.9348 (ptm) cc_final: 0.8996 (ptm) REVERT: B 66 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6770 (p90) outliers start: 32 outliers final: 27 residues processed: 74 average time/residue: 0.4102 time to fit residues: 38.6866 Evaluate side-chains 73 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 44 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 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 62 VAL Chi-restraints excluded: chain B residue 66 HIS 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 898 MET Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 62 VAL 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 Chi-restraints excluded: chain C residue 1090 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 148 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.037671 restraints weight = 93327.474| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 3.63 r_work: 0.2450 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27814 Z= 0.126 Angle : 0.534 12.565 37997 Z= 0.257 Chirality : 0.045 0.423 4467 Planarity : 0.003 0.037 4770 Dihedral : 7.511 115.383 5256 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.11 % Allowed : 8.80 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.15), residues: 3279 helix: 1.81 (0.21), residues: 717 sheet: 0.76 (0.20), residues: 642 loop : -1.03 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.020 0.001 TYR C 365 PHE 0.026 0.001 PHE A 562 TRP 0.010 0.001 TRP A 152 HIS 0.002 0.000 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00292 (27696) covalent geometry : angle 0.50050 (37686) SS BOND : bond 0.00309 ( 43) SS BOND : angle 0.95695 ( 86) hydrogen bonds : bond 0.04139 ( 1030) hydrogen bonds : angle 4.58612 ( 2904) link_BETA1-4 : bond 0.00255 ( 21) link_BETA1-4 : angle 1.79009 ( 63) link_NAG-ASN : bond 0.00412 ( 54) link_NAG-ASN : angle 2.63938 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5016.71 seconds wall clock time: 87 minutes 7.37 seconds (5227.37 seconds total)