Starting phenix.real_space_refine on Fri Mar 6 09:39:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sb4_24969/03_2026/7sb4_24969.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sb4_24969/03_2026/7sb4_24969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sb4_24969/03_2026/7sb4_24969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sb4_24969/03_2026/7sb4_24969.map" model { file = "/net/cci-nas-00/data/ceres_data/7sb4_24969/03_2026/7sb4_24969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sb4_24969/03_2026/7sb4_24969.cif" } resolution = 4.7 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= 0.000 sd= 0.005 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 189 5.16 5 C 18618 2.51 5 N 4778 2.21 5 O 5746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29331 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 9151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9151 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 5 Chain: "C" Number of atoms: 9134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9134 Classifications: {'peptide': 1173} Link IDs: {'PTRANS': 50, 'TRANS': 1122} Chain breaks: 6 Chain: "B" Number of atoms: 9178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9178 Classifications: {'peptide': 1180} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 172 Unusual residues: {'8Z9': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'8Z9': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'8Z9': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.36, per 1000 atoms: 0.22 Number of scatterers: 29331 At special positions: 0 Unit cell: (150.38, 164.8, 161.71, 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 189 16.00 O 5746 8.00 N 4778 7.00 C 18618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.02 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.11 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.08 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.04 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.04 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.04 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.05 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.05 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.02 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.08 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.02 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 173 " distance=2.02 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 260 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 308 " distance=2.06 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.09 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.04 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.04 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.05 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.07 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.04 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C 747 " - pdb=" SG CYS C 756 " distance=1.73 Simple disulfide: pdb=" SG CYS C 825 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C 830 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 937 " - pdb=" SG CYS C 948 " distance=2.09 Simple disulfide: pdb=" SG CYS C1125 " - pdb=" SG CYS C1136 " distance=2.02 Simple disulfide: pdb=" SG CYS C1175 " - pdb=" SG CYS C1220 " distance=2.02 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.02 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.04 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.05 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.02 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.05 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.04 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.02 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.04 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.07 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.04 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.03 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.02 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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-ASN " NAG A1401 " - " ASN A 137 " " NAG A1402 " - " ASN A 212 " " NAG A1403 " - " ASN A 713 " " NAG A1404 " - " ASN A 787 " " NAG A1405 " - " ASN A 936 " " NAG A1406 " - " ASN A1193 " " NAG A1407 " - " ASN A 675 " " NAG A1408 " - " ASN A 695 " " NAG A1409 " - " ASN A 648 " " NAG A1410 " - " ASN A 449 " " NAG A1411 " - " ASN A1223 " " NAG B1401 " - " ASN B 212 " " NAG B1402 " - " ASN B 449 " " NAG B1403 " - " ASN B 713 " " NAG B1404 " - " ASN B 787 " " NAG B1405 " - " ASN B 936 " " NAG B1406 " - " ASN B1193 " " NAG B1407 " - " ASN B 675 " " NAG B1408 " - " ASN B 695 " " NAG B1409 " - " ASN B 648 " " NAG B1410 " - " ASN B1223 " " NAG C1401 " - " ASN C 212 " " NAG C1402 " - " ASN C 449 " " NAG C1403 " - " ASN C 713 " " NAG C1404 " - " ASN C 787 " " NAG C1405 " - " ASN C 936 " " NAG C1406 " - " ASN C 675 " " NAG C1407 " - " ASN C 695 " " NAG C1408 " - " ASN C 648 " " NAG C1409 " - " ASN C 371 " " NAG C1410 " - " ASN C1223 " " NAG D 1 " - " ASN A 738 " " NAG E 1 " - " ASN A 206 " " NAG F 1 " - " ASN A 371 " " NAG G 1 " - " ASN C 137 " " NAG I 1 " - " ASN C 738 " " NAG J 1 " - " ASN C1193 " " NAG K 1 " - " ASN C 206 " " NAG M 1 " - " ASN B 137 " " NAG N 1 " - " ASN B 371 " " NAG O 1 " - " ASN B 738 " " NAG P 1 " - " ASN B 206 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 79 sheets defined 25.8% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 357 through 360 removed outlier: 4.064A pdb=" N TRP A 360 " --> pdb=" O PRO A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.546A pdb=" N LEU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 833 through 841 Processing helix chain 'A' and resid 843 through 874 removed outlier: 3.565A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 884 Processing helix chain 'A' and resid 913 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 945 through 953 Processing helix chain 'A' and resid 963 through 980 removed outlier: 3.736A pdb=" N SER A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1035 through 1059 removed outlier: 3.671A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 Processing helix chain 'A' and resid 1078 through 1125 removed outlier: 3.910A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 422 through 429 Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 825 through 828 Processing helix chain 'C' and resid 833 through 840 Processing helix chain 'C' and resid 843 through 874 removed outlier: 3.578A pdb=" N CYS C 847 " --> pdb=" O TYR C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 884 Processing helix chain 'C' and resid 913 through 922 Processing helix chain 'C' and resid 926 through 934 Processing helix chain 'C' and resid 945 through 953 Processing helix chain 'C' and resid 963 through 980 Processing helix chain 'C' and resid 990 through 1001 Processing helix chain 'C' and resid 1005 through 1012 Processing helix chain 'C' and resid 1012 through 1030 Processing helix chain 'C' and resid 1035 through 1058 Processing helix chain 'C' and resid 1059 through 1061 No H-bonds generated for 'chain 'C' and resid 1059 through 1061' Processing helix chain 'C' and resid 1069 through 1077 Processing helix chain 'C' and resid 1078 through 1126 removed outlier: 5.002A pdb=" N ALA C1084 " --> pdb=" O PRO C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1212 No H-bonds generated for 'chain 'C' and resid 1210 through 1212' Processing helix chain 'B' and resid 93 through 96 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 357 through 360 removed outlier: 3.994A pdb=" N TRP B 360 " --> pdb=" O PRO B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 422 through 429 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 458 through 464 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 824 through 830 Processing helix chain 'B' and resid 833 through 840 Processing helix chain 'B' and resid 843 through 874 removed outlier: 3.632A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 913 through 922 Processing helix chain 'B' and resid 926 through 937 removed outlier: 4.223A pdb=" N ASN B 935 " --> pdb=" O VAL B 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS B 937 " --> pdb=" O ALA B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 953 Processing helix chain 'B' and resid 963 through 980 Processing helix chain 'B' and resid 990 through 1003 Processing helix chain 'B' and resid 1005 through 1012 Processing helix chain 'B' and resid 1012 through 1030 Processing helix chain 'B' and resid 1035 through 1060 Processing helix chain 'B' and resid 1069 through 1077 Processing helix chain 'B' and resid 1078 through 1125 removed outlier: 3.800A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing helix chain 'H' and resid 70 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 4.457A pdb=" N PHE A 240 " --> pdb=" O TYR A 55 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA A 229 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN A 243 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE A 227 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.665A pdb=" N THR A 178 " --> pdb=" O THR A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 321 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 335 removed outlier: 5.824A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 658 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.596A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER A 438 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N CYS A 386 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN A 440 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE A 384 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR A 442 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.596A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AB5, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AB6, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AB7, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AB8, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AB9, first strand: chain 'A' and resid 743 through 744 Processing sheet with id=AC1, first strand: chain 'A' and resid 749 through 752 removed outlier: 4.229A pdb=" N LEU A 749 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 784 through 786 removed outlier: 6.248A pdb=" N ASN A 784 " --> pdb=" O LEU B 878 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 797 through 802 Processing sheet with id=AC4, first strand: chain 'A' and resid 805 through 815 removed outlier: 7.276A pdb=" N GLY A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASN A1148 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR A1154 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A1146 " --> pdb=" O TYR A1154 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A1156 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A1144 " --> pdb=" O ILE A1156 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A1158 " --> pdb=" O ILE A1142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 820 through 823 removed outlier: 3.861A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 877 through 879 Processing sheet with id=AC7, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AC8, first strand: chain 'A' and resid 1214 through 1217 removed outlier: 3.716A pdb=" N ARG A1180 " --> pdb=" O ILE A1176 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1187 through 1192 removed outlier: 4.219A pdb=" N GLY A1200 " --> pdb=" O TYR A1205 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A1205 " --> pdb=" O GLY A1200 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 43 through 44 removed outlier: 4.035A pdb=" N ALA C 43 " --> pdb=" O TYR C 79 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR C 78 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 227 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN C 243 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA C 229 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 64 through 73 removed outlier: 3.607A pdb=" N ASN C 294 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 114 through 118 Processing sheet with id=AD4, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.515A pdb=" N VAL C 167 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS C 204 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL C 165 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN C 206 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 163 " --> pdb=" O ASN C 206 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR C 208 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY C 161 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 191 through 193 removed outlier: 7.877A pdb=" N HIS C 193 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N TYR C 175 " --> pdb=" O HIS C 193 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N THR C 259 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 178 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 318 through 321 Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AD8, first strand: chain 'C' and resid 331 through 335 removed outlier: 6.836A pdb=" N ALA C 331 " --> pdb=" O ASN C 632 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASP C 634 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 333 " --> pdb=" O ASP C 634 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 676 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.695A pdb=" N VAL C 354 " --> pdb=" O SER C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 365 removed outlier: 6.680A pdb=" N PHE C 399 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 608 " --> pdb=" O PHE C 399 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN C 444 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA C 381 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 369 through 370 removed outlier: 6.680A pdb=" N PHE C 399 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 608 " --> pdb=" O PHE C 399 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 484 through 488 Processing sheet with id=AE4, first strand: chain 'C' and resid 492 through 493 Processing sheet with id=AE5, first strand: chain 'C' and resid 520 through 521 Processing sheet with id=AE6, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AE7, first strand: chain 'C' and resid 743 through 744 removed outlier: 6.409A pdb=" N TYR C 755 " --> pdb=" O VAL C 751 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 797 through 802 Processing sheet with id=AE9, first strand: chain 'C' and resid 805 through 815 removed outlier: 7.297A pdb=" N GLY C1152 " --> pdb=" O ASN C1148 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASN C1148 " --> pdb=" O GLY C1152 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR C1154 " --> pdb=" O VAL C1146 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C1146 " --> pdb=" O TYR C1154 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C1156 " --> pdb=" O SER C1144 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C1144 " --> pdb=" O ILE C1156 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C1158 " --> pdb=" O ILE C1142 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 820 through 823 removed outlier: 3.949A pdb=" N LYS C 820 " --> pdb=" O LEU C 958 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 877 through 879 Processing sheet with id=AF3, first strand: chain 'C' and resid 889 through 890 Processing sheet with id=AF4, first strand: chain 'C' and resid 1214 through 1216 Processing sheet with id=AF5, first strand: chain 'C' and resid 1187 through 1192 Processing sheet with id=AF6, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AF7, first strand: chain 'B' and resid 40 through 44 removed outlier: 6.904A pdb=" N SER B 41 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASN B 81 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 43 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR B 78 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE B 227 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN B 243 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 229 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR B 53 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N PHE B 240 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 64 through 72 removed outlier: 3.604A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 101 through 102 removed outlier: 7.708A pdb=" N GLY B 161 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR B 208 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU B 163 " --> pdb=" O ASN B 206 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 206 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B 165 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 204 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 167 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AG2, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.424A pdb=" N THR B 178 " --> pdb=" O THR B 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'B' and resid 318 through 321 Processing sheet with id=AG4, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AG5, first strand: chain 'B' and resid 331 through 335 removed outlier: 3.581A pdb=" N ALA B 331 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.696A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.549A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.549A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AH1, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AH2, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AH3, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AH4, first strand: chain 'B' and resid 571 through 572 removed outlier: 3.717A pdb=" N THR B 577 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 737 through 744 removed outlier: 6.765A pdb=" N TYR B 737 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN B 777 " --> pdb=" O TYR B 737 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N SER B 739 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 749 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 797 through 815 removed outlier: 6.928A pdb=" N GLU B 798 " --> pdb=" O LYS B1169 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS B1169 " --> pdb=" O GLU B 798 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLN B 800 " --> pdb=" O THR B1167 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1167 " --> pdb=" O GLN B 800 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR B1165 " --> pdb=" O PRO B 802 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU B 804 " --> pdb=" O THR B1163 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B1143 " --> pdb=" O PHE B1158 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.044A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 889 through 890 Processing sheet with id=AH9, first strand: chain 'B' and resid 1214 through 1217 removed outlier: 5.757A pdb=" N CYS B1175 " --> pdb=" O ALA B1227 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 4.828A pdb=" N GLY B1200 " --> pdb=" O TYR B1205 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR B1205 " --> pdb=" O GLY B1200 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 20 through 23 Processing sheet with id=AI3, first strand: chain 'H' and resid 50 through 51 removed outlier: 3.811A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N UNK H 33 " --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N UNK H 96 " --> pdb=" O UNK H 33 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 50 through 51 removed outlier: 3.811A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N UNK H 33 " --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N UNK H 96 " --> pdb=" O UNK H 33 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.566A pdb=" N UNK L 22 " --> pdb=" O UNK L 5 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.566A pdb=" N UNK L 22 " --> pdb=" O UNK L 5 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 9 through 10 removed outlier: 5.007A pdb=" N UNK L 83 " --> pdb=" O UNK L 94 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N UNK L 96 " --> pdb=" O UNK L 81 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N UNK L 81 " --> pdb=" O UNK L 96 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N UNK L 98 " --> pdb=" O UNK L 79 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N UNK L 79 " --> pdb=" O UNK L 98 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) 1227 hydrogen bonds defined for protein. 3345 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: 8.09 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 6882 1.32 - 1.47: 10544 1.47 - 1.62: 12288 1.62 - 1.77: 32 1.77 - 1.92: 216 Bond restraints: 29962 Sorted by residual: bond pdb=" CB HIS C 483 " pdb=" CG HIS C 483 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.27e+01 bond pdb=" CB HIS C 219 " pdb=" CG HIS C 219 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.56e+01 bond pdb=" CB ASN A1213 " pdb=" CG ASN A1213 " ideal model delta sigma weight residual 1.516 1.373 0.143 2.50e-02 1.60e+03 3.28e+01 bond pdb=" CB HIS A 219 " pdb=" CG HIS A 219 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 2.99e+01 bond pdb=" N PRO B 474 " pdb=" CD PRO B 474 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.65e+01 ... (remaining 29957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 36700 2.88 - 5.75: 3676 5.75 - 8.63: 377 8.63 - 11.50: 42 11.50 - 14.38: 3 Bond angle restraints: 40798 Sorted by residual: angle pdb=" C PRO A 959 " pdb=" N PRO A 960 " pdb=" CA PRO A 960 " ideal model delta sigma weight residual 120.03 129.06 -9.03 9.90e-01 1.02e+00 8.33e+01 angle pdb=" C PRO C 959 " pdb=" N PRO C 960 " pdb=" CA PRO C 960 " ideal model delta sigma weight residual 120.21 128.75 -8.54 9.60e-01 1.09e+00 7.92e+01 angle pdb=" N THR B 577 " pdb=" CA THR B 577 " pdb=" C THR B 577 " ideal model delta sigma weight residual 109.24 96.54 12.70 1.51e+00 4.39e-01 7.08e+01 angle pdb=" C PRO A 37 " pdb=" N PRO A 38 " pdb=" CA PRO A 38 " ideal model delta sigma weight residual 118.97 127.64 -8.67 1.04e+00 9.25e-01 6.96e+01 angle pdb=" C ALA C1227 " pdb=" N PRO C1228 " pdb=" CA PRO C1228 " ideal model delta sigma weight residual 119.56 128.04 -8.48 1.02e+00 9.61e-01 6.92e+01 ... (remaining 40793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 18338 34.94 - 69.88: 191 69.88 - 104.81: 34 104.81 - 139.75: 6 139.75 - 174.69: 2 Dihedral angle restraints: 18571 sinusoidal: 7634 harmonic: 10937 Sorted by residual: dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS C 576 " pdb=" CB CYS C 576 " ideal model delta sinusoidal sigma weight residual -86.00 -141.84 55.84 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CB CYS C 535 " pdb=" SG CYS C 535 " pdb=" SG CYS C 548 " pdb=" CB CYS C 548 " ideal model delta sinusoidal sigma weight residual 93.00 147.45 -54.45 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS A 630 " pdb=" SG CYS A 630 " pdb=" SG CYS A 683 " pdb=" CB CYS A 683 " ideal model delta sinusoidal sigma weight residual -86.00 -136.81 50.81 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 18568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.964: 4788 0.964 - 1.928: 1 1.928 - 2.891: 0 2.891 - 3.855: 0 3.855 - 4.819: 1 Chirality restraints: 4790 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 2.42 -4.82 2.00e-02 2.50e+03 5.81e+04 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 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 ... (remaining 4787 not shown) Planarity restraints: 5248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1404 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1404 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1404 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG A1404 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG A1404 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1402 " 0.327 2.00e-02 2.50e+03 2.77e-01 9.61e+02 pdb=" C7 NAG A1402 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A1402 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG A1402 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG A1402 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.312 2.00e-02 2.50e+03 2.65e-01 8.78e+02 pdb=" C7 NAG M 2 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.180 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.461 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.049 2.00e-02 2.50e+03 ... (remaining 5245 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6261 2.77 - 3.31: 28348 3.31 - 3.84: 50629 3.84 - 4.37: 62061 4.37 - 4.90: 98603 Nonbonded interactions: 245902 Sorted by model distance: nonbonded pdb=" O3 NAG M 2 " pdb=" O7 NAG M 2 " model vdw 2.242 3.040 nonbonded pdb=" N THR B 577 " pdb=" O THR B 577 " model vdw 2.361 2.496 nonbonded pdb=" N VAL C 136 " pdb=" O VAL C 136 " model vdw 2.364 2.496 nonbonded pdb=" N VAL B 136 " pdb=" O VAL B 136 " model vdw 2.384 2.496 nonbonded pdb=" O SER C 41 " pdb=" OG SER C 41 " model vdw 2.385 3.040 ... (remaining 245897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 33 or resid 38 through 473 or resid 481 through \ 901 or resid 910 through 1410)) selection = (chain 'B' and (resid 15 through 33 or resid 38 through 150 or resid 158 through \ 473 or resid 481 through 504 or resid 518 through 762 or resid 772 through 901 \ or resid 910 through 1410)) selection = (chain 'C' and (resid 15 through 504 or resid 518 through 762 or resid 772 throu \ gh 1410)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 17 through 115) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 28.280 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 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 : 0.020 0.296 30080 Z= 1.068 Angle : 1.799 16.221 41089 Z= 1.193 Chirality : 0.136 4.819 4790 Planarity : 0.015 0.302 5206 Dihedral : 11.157 174.688 11370 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 3491 helix: 0.23 (0.16), residues: 831 sheet: 0.90 (0.18), residues: 734 loop : 0.34 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 454 TYR 0.086 0.009 TYR A 79 PHE 0.054 0.006 PHE B 464 TRP 0.063 0.010 TRP B 586 HIS 0.022 0.003 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.01968 (29962) covalent geometry : angle 1.78769 (40798) SS BOND : bond 0.04233 ( 63) SS BOND : angle 2.37868 ( 126) hydrogen bonds : bond 0.16615 ( 1183) hydrogen bonds : angle 8.39895 ( 3345) link_BETA1-4 : bond 0.06002 ( 13) link_BETA1-4 : angle 5.06170 ( 39) link_NAG-ASN : bond 0.06431 ( 42) link_NAG-ASN : angle 2.63197 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 812 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.7437 (tt) cc_final: 0.7015 (tt) REVERT: A 104 ILE cc_start: 0.8238 (mm) cc_final: 0.7920 (pt) REVERT: A 129 ILE cc_start: 0.8159 (pt) cc_final: 0.7788 (pt) REVERT: A 145 GLN cc_start: 0.7394 (pt0) cc_final: 0.7192 (tt0) REVERT: A 165 VAL cc_start: 0.6597 (t) cc_final: 0.6371 (p) REVERT: A 263 ARG cc_start: 0.7104 (mmt180) cc_final: 0.6705 (mtm180) REVERT: A 296 VAL cc_start: 0.5529 (t) cc_final: 0.4554 (t) REVERT: A 332 ASP cc_start: 0.6669 (m-30) cc_final: 0.6348 (m-30) REVERT: A 375 LEU cc_start: 0.7848 (tp) cc_final: 0.7573 (mp) REVERT: A 376 MET cc_start: 0.7476 (mtm) cc_final: 0.5604 (ptp) REVERT: A 397 MET cc_start: 0.8095 (ttm) cc_final: 0.7017 (tpp) REVERT: A 415 VAL cc_start: 0.7283 (t) cc_final: 0.7077 (t) REVERT: A 433 ASP cc_start: 0.8458 (t0) cc_final: 0.8080 (t0) REVERT: A 625 ILE cc_start: 0.8395 (mt) cc_final: 0.8098 (tp) REVERT: A 663 ASN cc_start: 0.6674 (m-40) cc_final: 0.6320 (m-40) REVERT: A 667 TYR cc_start: 0.5206 (p90) cc_final: 0.4959 (p90) REVERT: A 734 VAL cc_start: 0.7743 (t) cc_final: 0.7363 (p) REVERT: A 807 ILE cc_start: 0.8276 (mt) cc_final: 0.7967 (tp) REVERT: A 849 ASN cc_start: 0.7881 (m-40) cc_final: 0.7356 (m-40) REVERT: A 873 MET cc_start: 0.7130 (ppp) cc_final: 0.6656 (ppp) REVERT: A 892 ASP cc_start: 0.5520 (t0) cc_final: 0.4981 (t0) REVERT: A 916 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 943 ILE cc_start: 0.5931 (mm) cc_final: 0.5688 (tp) REVERT: A 970 TYR cc_start: 0.8147 (m-80) cc_final: 0.7549 (m-80) REVERT: A 1010 SER cc_start: 0.7565 (t) cc_final: 0.6766 (m) REVERT: A 1061 ASN cc_start: 0.7876 (m110) cc_final: 0.7365 (m110) REVERT: A 1081 GLU cc_start: 0.7035 (tp30) cc_final: 0.6276 (mp0) REVERT: A 1089 LEU cc_start: 0.8186 (mt) cc_final: 0.7847 (tp) REVERT: A 1134 ASN cc_start: 0.8387 (m-40) cc_final: 0.8023 (m110) REVERT: A 1230 VAL cc_start: 0.7040 (t) cc_final: 0.6145 (t) REVERT: C 16 ILE cc_start: 0.8355 (mm) cc_final: 0.7863 (mm) REVERT: C 45 VAL cc_start: 0.6960 (t) cc_final: 0.6615 (t) REVERT: C 60 VAL cc_start: 0.7366 (p) cc_final: 0.6833 (p) REVERT: C 89 LYS cc_start: 0.5830 (mmtm) cc_final: 0.5507 (pptt) REVERT: C 125 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7678 (pm20) REVERT: C 166 SER cc_start: 0.8380 (p) cc_final: 0.7982 (m) REVERT: C 170 TYR cc_start: 0.5756 (p90) cc_final: 0.5319 (p90) REVERT: C 177 HIS cc_start: 0.7729 (m90) cc_final: 0.6942 (m90) REVERT: C 192 TRP cc_start: 0.6996 (p-90) cc_final: 0.6377 (p-90) REVERT: C 307 LYS cc_start: 0.7345 (mttt) cc_final: 0.7114 (mttt) REVERT: C 321 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7636 (mm-30) REVERT: C 346 GLU cc_start: 0.7205 (mp0) cc_final: 0.6494 (pp20) REVERT: C 382 ASP cc_start: 0.8521 (m-30) cc_final: 0.8070 (t0) REVERT: C 397 MET cc_start: 0.6334 (ttm) cc_final: 0.6039 (ttm) REVERT: C 437 THR cc_start: 0.7747 (m) cc_final: 0.7436 (t) REVERT: C 440 GLN cc_start: 0.7670 (mp10) cc_final: 0.7437 (mp10) REVERT: C 445 LEU cc_start: 0.6810 (mt) cc_final: 0.6390 (mt) REVERT: C 450 VAL cc_start: 0.8062 (t) cc_final: 0.7799 (m) REVERT: C 546 TYR cc_start: 0.7030 (m-80) cc_final: 0.6436 (p90) REVERT: C 602 ASN cc_start: 0.7282 (t0) cc_final: 0.6530 (t0) REVERT: C 626 LYS cc_start: 0.8180 (mttp) cc_final: 0.7537 (mmmt) REVERT: C 679 MET cc_start: 0.7979 (mmm) cc_final: 0.7436 (mmm) REVERT: C 724 ASN cc_start: 0.5806 (m-40) cc_final: 0.5397 (m110) REVERT: C 824 ASP cc_start: 0.8136 (t0) cc_final: 0.7700 (t0) REVERT: C 881 LYS cc_start: 0.7738 (mttm) cc_final: 0.6928 (mtmt) REVERT: C 882 LEU cc_start: 0.8438 (mt) cc_final: 0.8210 (mp) REVERT: C 883 LYS cc_start: 0.6895 (mmmt) cc_final: 0.6617 (tppt) REVERT: C 965 ASN cc_start: 0.7184 (m-40) cc_final: 0.6895 (m110) REVERT: C 989 VAL cc_start: 0.7949 (t) cc_final: 0.6544 (t) REVERT: C 994 ASN cc_start: 0.8373 (t0) cc_final: 0.8068 (m-40) REVERT: C 1002 LEU cc_start: 0.7505 (mt) cc_final: 0.7253 (tp) REVERT: C 1104 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7243 (tt0) REVERT: C 1113 PHE cc_start: 0.7656 (t80) cc_final: 0.7174 (t80) REVERT: C 1133 ILE cc_start: 0.7848 (mm) cc_final: 0.7203 (mm) REVERT: C 1165 TYR cc_start: 0.6403 (m-80) cc_final: 0.6156 (m-80) REVERT: C 1197 MET cc_start: 0.5926 (mtp) cc_final: 0.5588 (mtt) REVERT: B 82 MET cc_start: 0.7144 (mmm) cc_final: 0.6466 (tpp) REVERT: B 88 ASP cc_start: 0.8352 (t0) cc_final: 0.8081 (t70) REVERT: B 164 GLU cc_start: 0.5740 (mt-10) cc_final: 0.5499 (pt0) REVERT: B 170 TYR cc_start: 0.5389 (m-80) cc_final: 0.5011 (m-80) REVERT: B 172 MET cc_start: 0.8282 (mtp) cc_final: 0.7872 (mtp) REVERT: B 209 TYR cc_start: 0.7372 (p90) cc_final: 0.7096 (p90) REVERT: B 217 TYR cc_start: 0.6448 (m-80) cc_final: 0.5915 (m-80) REVERT: B 287 ASN cc_start: 0.6937 (t0) cc_final: 0.5881 (m-40) REVERT: B 299 MET cc_start: 0.7695 (mmm) cc_final: 0.6523 (ttp) REVERT: B 383 SER cc_start: 0.7192 (t) cc_final: 0.6453 (p) REVERT: B 452 VAL cc_start: 0.7306 (t) cc_final: 0.6803 (p) REVERT: B 485 VAL cc_start: 0.7097 (t) cc_final: 0.6858 (m) REVERT: B 554 LEU cc_start: 0.8483 (mt) cc_final: 0.8236 (mm) REVERT: B 589 ASP cc_start: 0.5980 (t0) cc_final: 0.5202 (m-30) REVERT: B 655 TRP cc_start: 0.5651 (p-90) cc_final: 0.5419 (p-90) REVERT: B 656 GLN cc_start: 0.7720 (mt0) cc_final: 0.6302 (mt0) REVERT: B 669 PHE cc_start: 0.7260 (t80) cc_final: 0.6786 (t80) REVERT: B 737 TYR cc_start: 0.7367 (t80) cc_final: 0.7096 (m-10) REVERT: B 798 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7291 (mm-30) REVERT: B 812 GLU cc_start: 0.7578 (tp30) cc_final: 0.6728 (mt-10) REVERT: B 853 ILE cc_start: 0.7337 (mt) cc_final: 0.6879 (mt) REVERT: B 874 ASN cc_start: 0.6720 (t0) cc_final: 0.6482 (t0) REVERT: B 881 LYS cc_start: 0.6830 (mttm) cc_final: 0.6429 (mttp) REVERT: B 892 ASP cc_start: 0.7659 (m-30) cc_final: 0.7085 (t0) REVERT: B 915 ILE cc_start: 0.8518 (mt) cc_final: 0.7905 (mt) REVERT: B 951 SER cc_start: 0.8946 (t) cc_final: 0.8648 (m) REVERT: B 998 ARG cc_start: 0.7639 (mmm160) cc_final: 0.6865 (tpp-160) REVERT: B 1005 THR cc_start: 0.7659 (m) cc_final: 0.7342 (p) REVERT: B 1126 VAL cc_start: 0.7680 (t) cc_final: 0.7478 (t) REVERT: B 1135 PHE cc_start: 0.7383 (t80) cc_final: 0.6773 (t80) REVERT: B 1197 MET cc_start: 0.8535 (mtp) cc_final: 0.8316 (mmm) REVERT: B 1224 TYR cc_start: 0.6623 (m-10) cc_final: 0.6309 (m-10) outliers start: 0 outliers final: 0 residues processed: 812 average time/residue: 0.1838 time to fit residues: 238.1417 Evaluate side-chains 343 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 440 GLN A 705 ASN A 996 GLN C 105 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 714 ASN C 724 ASN C 996 GLN C1000 ASN C1028 GLN C1057 GLN C1058 GLN C1117 GLN C1138 ASN C1148 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 966 GLN B 994 ASN B1018 ASN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 ASN B1103 GLN ** B1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1194 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.056666 restraints weight = 131552.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.057970 restraints weight = 79367.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.058858 restraints weight = 53468.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059497 restraints weight = 39429.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059900 restraints weight = 31366.129| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 30080 Z= 0.183 Angle : 0.796 16.321 41089 Z= 0.404 Chirality : 0.053 1.130 4790 Planarity : 0.005 0.053 5206 Dihedral : 8.958 161.479 5211 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.16 % Allowed : 2.18 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3491 helix: 1.33 (0.18), residues: 832 sheet: 0.64 (0.18), residues: 721 loop : -0.05 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 912 TYR 0.028 0.002 TYR A 651 PHE 0.038 0.002 PHE C1113 TRP 0.028 0.003 TRP C 460 HIS 0.008 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00392 (29962) covalent geometry : angle 0.76031 (40798) SS BOND : bond 0.00288 ( 63) SS BOND : angle 1.10832 ( 126) hydrogen bonds : bond 0.06142 ( 1183) hydrogen bonds : angle 6.22589 ( 3345) link_BETA1-4 : bond 0.00780 ( 13) link_BETA1-4 : angle 2.61322 ( 39) link_NAG-ASN : bond 0.00672 ( 42) link_NAG-ASN : angle 4.00810 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 461 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6382 (mmm) cc_final: 0.6122 (mmm) REVERT: A 194 MET cc_start: 0.5511 (tpt) cc_final: 0.4101 (tmm) REVERT: A 254 TYR cc_start: 0.5163 (t80) cc_final: 0.4657 (t80) REVERT: A 263 ARG cc_start: 0.7139 (mmt180) cc_final: 0.6934 (tpt170) REVERT: A 277 LEU cc_start: 0.8039 (mt) cc_final: 0.7829 (mt) REVERT: A 433 ASP cc_start: 0.8741 (t0) cc_final: 0.8528 (t0) REVERT: A 726 PHE cc_start: 0.3880 (m-10) cc_final: 0.3448 (m-80) REVERT: A 892 ASP cc_start: 0.5174 (t0) cc_final: 0.4740 (t0) REVERT: A 916 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 1138 ASN cc_start: 0.7429 (m-40) cc_final: 0.6887 (p0) REVERT: A 1217 MET cc_start: 0.6193 (ptp) cc_final: 0.5962 (ptp) REVERT: C 60 VAL cc_start: 0.7884 (p) cc_final: 0.7663 (p) REVERT: C 170 TYR cc_start: 0.5238 (p90) cc_final: 0.4931 (p90) REVERT: C 258 LEU cc_start: 0.6862 (tp) cc_final: 0.6579 (tp) REVERT: C 280 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6569 (ttm-80) REVERT: C 346 GLU cc_start: 0.7141 (mp0) cc_final: 0.6731 (tm-30) REVERT: C 445 LEU cc_start: 0.7661 (mt) cc_final: 0.7401 (mt) REVERT: C 467 ILE cc_start: 0.7524 (mm) cc_final: 0.6794 (mm) REVERT: C 492 PHE cc_start: 0.6065 (m-80) cc_final: 0.5740 (m-10) REVERT: C 602 ASN cc_start: 0.7906 (t0) cc_final: 0.5454 (t0) REVERT: C 626 LYS cc_start: 0.8226 (mttp) cc_final: 0.7687 (mmmt) REVERT: C 824 ASP cc_start: 0.8598 (t0) cc_final: 0.8180 (t0) REVERT: C 868 VAL cc_start: 0.9033 (t) cc_final: 0.8697 (p) REVERT: C 965 ASN cc_start: 0.7028 (m-40) cc_final: 0.6618 (m110) REVERT: C 1002 LEU cc_start: 0.8534 (mt) cc_final: 0.7841 (tp) REVERT: C 1005 THR cc_start: 0.8385 (t) cc_final: 0.8152 (m) REVERT: C 1197 MET cc_start: 0.6631 (mtp) cc_final: 0.6230 (mtt) REVERT: B 66 LEU cc_start: 0.7785 (mp) cc_final: 0.7510 (mp) REVERT: B 82 MET cc_start: 0.7069 (mmm) cc_final: 0.6635 (tpp) REVERT: B 163 LEU cc_start: 0.8039 (tp) cc_final: 0.7723 (tp) REVERT: B 170 TYR cc_start: 0.5362 (m-80) cc_final: 0.4110 (m-80) REVERT: B 172 MET cc_start: 0.7413 (mtp) cc_final: 0.7099 (mtm) REVERT: B 194 MET cc_start: 0.4024 (ttm) cc_final: 0.3632 (mtp) REVERT: B 209 TYR cc_start: 0.7739 (p90) cc_final: 0.7314 (p90) REVERT: B 217 TYR cc_start: 0.6110 (m-80) cc_final: 0.5425 (m-80) REVERT: B 287 ASN cc_start: 0.6183 (t0) cc_final: 0.5941 (m-40) REVERT: B 372 MET cc_start: 0.6869 (tpp) cc_final: 0.6422 (tpp) REVERT: B 383 SER cc_start: 0.7223 (t) cc_final: 0.6907 (p) REVERT: B 589 ASP cc_start: 0.5975 (t0) cc_final: 0.5692 (m-30) REVERT: B 669 PHE cc_start: 0.6154 (t80) cc_final: 0.5814 (t80) REVERT: B 812 GLU cc_start: 0.7268 (tp30) cc_final: 0.6527 (mt-10) REVERT: B 846 PHE cc_start: 0.8392 (m-80) cc_final: 0.7934 (m-80) REVERT: B 848 ASP cc_start: 0.6579 (m-30) cc_final: 0.6329 (m-30) REVERT: B 862 ASP cc_start: 0.7240 (t0) cc_final: 0.6183 (t70) REVERT: B 874 ASN cc_start: 0.7118 (t0) cc_final: 0.6547 (t0) REVERT: B 998 ARG cc_start: 0.7399 (mmm160) cc_final: 0.6918 (tpp-160) REVERT: B 1005 THR cc_start: 0.7746 (m) cc_final: 0.7329 (m) REVERT: B 1135 PHE cc_start: 0.8318 (t80) cc_final: 0.8072 (t80) REVERT: B 1197 MET cc_start: 0.7920 (mtp) cc_final: 0.7144 (mmm) outliers start: 5 outliers final: 1 residues processed: 466 average time/residue: 0.1756 time to fit residues: 135.3517 Evaluate side-chains 256 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 259 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 338 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 266 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 187 HIS A 219 HIS A 444 ASN A 641 GLN A 809 ASN A 849 ASN A1012 ASN A1103 GLN C 160 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN B 160 GLN B 421 ASN B 581 GLN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN B1085 GLN B1147 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053647 restraints weight = 136988.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.055157 restraints weight = 86420.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055854 restraints weight = 54311.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056228 restraints weight = 44818.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056534 restraints weight = 35253.516| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 30080 Z= 0.199 Angle : 0.730 11.105 41089 Z= 0.372 Chirality : 0.049 0.717 4790 Planarity : 0.005 0.043 5206 Dihedral : 8.006 137.047 5211 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3491 helix: 1.30 (0.18), residues: 843 sheet: 0.50 (0.18), residues: 727 loop : -0.26 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 431 TYR 0.024 0.002 TYR B 79 PHE 0.023 0.002 PHE A1063 TRP 0.020 0.002 TRP B 586 HIS 0.006 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00441 (29962) covalent geometry : angle 0.70223 (40798) SS BOND : bond 0.00824 ( 63) SS BOND : angle 1.28269 ( 126) hydrogen bonds : bond 0.05369 ( 1183) hydrogen bonds : angle 5.73582 ( 3345) link_BETA1-4 : bond 0.00554 ( 13) link_BETA1-4 : angle 2.10231 ( 39) link_NAG-ASN : bond 0.00772 ( 42) link_NAG-ASN : angle 3.29862 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6905 (mmm) cc_final: 0.6602 (mmm) REVERT: A 194 MET cc_start: 0.5496 (tpt) cc_final: 0.4579 (tmm) REVERT: A 307 LYS cc_start: 0.7346 (mtpt) cc_final: 0.7002 (mtmt) REVERT: A 599 ILE cc_start: 0.7719 (mt) cc_final: 0.7412 (mt) REVERT: A 679 MET cc_start: 0.7938 (mmm) cc_final: 0.7455 (mtt) REVERT: A 916 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7523 (mt-10) REVERT: A 961 LEU cc_start: 0.7308 (tp) cc_final: 0.6890 (tp) REVERT: A 1063 PHE cc_start: 0.8446 (m-80) cc_final: 0.8199 (m-10) REVERT: A 1119 MET cc_start: 0.7728 (mtm) cc_final: 0.7499 (mtm) REVERT: A 1138 ASN cc_start: 0.7831 (m-40) cc_final: 0.7038 (p0) REVERT: C 54 TYR cc_start: 0.6384 (p90) cc_final: 0.6031 (p90) REVERT: C 175 TYR cc_start: 0.7234 (m-80) cc_final: 0.6861 (m-80) REVERT: C 248 MET cc_start: 0.7625 (ppp) cc_final: 0.7129 (ppp) REVERT: C 346 GLU cc_start: 0.7581 (mp0) cc_final: 0.7140 (tm-30) REVERT: C 538 ASP cc_start: 0.6976 (m-30) cc_final: 0.5982 (p0) REVERT: C 602 ASN cc_start: 0.7408 (t0) cc_final: 0.6725 (t0) REVERT: C 626 LYS cc_start: 0.8389 (mttp) cc_final: 0.7758 (mmmt) REVERT: C 646 GLU cc_start: 0.6956 (tp30) cc_final: 0.6490 (tm-30) REVERT: C 824 ASP cc_start: 0.8684 (t0) cc_final: 0.8288 (t0) REVERT: C 1002 LEU cc_start: 0.8419 (mt) cc_final: 0.7967 (tp) REVERT: C 1119 MET cc_start: 0.6702 (mtp) cc_final: 0.6402 (mtt) REVERT: C 1197 MET cc_start: 0.6712 (mtp) cc_final: 0.6134 (mtm) REVERT: B 29 SER cc_start: 0.6585 (p) cc_final: 0.6289 (p) REVERT: B 32 ASN cc_start: 0.7561 (m-40) cc_final: 0.6443 (t0) REVERT: B 82 MET cc_start: 0.7192 (mmm) cc_final: 0.6976 (tpp) REVERT: B 209 TYR cc_start: 0.8010 (p90) cc_final: 0.7491 (p90) REVERT: B 217 TYR cc_start: 0.6249 (m-80) cc_final: 0.5612 (m-80) REVERT: B 287 ASN cc_start: 0.6208 (t0) cc_final: 0.6007 (m-40) REVERT: B 296 VAL cc_start: 0.8691 (t) cc_final: 0.8290 (t) REVERT: B 332 ASP cc_start: 0.7466 (m-30) cc_final: 0.6829 (m-30) REVERT: B 369 ASN cc_start: 0.6783 (m-40) cc_final: 0.6472 (m-40) REVERT: B 383 SER cc_start: 0.7235 (t) cc_final: 0.6943 (p) REVERT: B 470 SER cc_start: 0.7571 (m) cc_final: 0.7234 (t) REVERT: B 542 PHE cc_start: 0.5426 (t80) cc_final: 0.5145 (t80) REVERT: B 656 GLN cc_start: 0.7806 (mt0) cc_final: 0.6859 (mt0) REVERT: B 669 PHE cc_start: 0.6228 (t80) cc_final: 0.5985 (t80) REVERT: B 717 ILE cc_start: 0.7654 (mm) cc_final: 0.7426 (pt) REVERT: B 812 GLU cc_start: 0.7469 (tp30) cc_final: 0.6690 (mt-10) REVERT: B 848 ASP cc_start: 0.6032 (m-30) cc_final: 0.5790 (m-30) REVERT: B 853 ILE cc_start: 0.7318 (mt) cc_final: 0.7054 (mt) REVERT: B 862 ASP cc_start: 0.6876 (t0) cc_final: 0.6644 (t0) REVERT: B 874 ASN cc_start: 0.7363 (t0) cc_final: 0.6738 (t0) REVERT: B 882 LEU cc_start: 0.7865 (mm) cc_final: 0.7635 (pp) REVERT: B 998 ARG cc_start: 0.7196 (mmm160) cc_final: 0.6936 (tpp-160) REVERT: B 1005 THR cc_start: 0.7355 (m) cc_final: 0.6858 (p) REVERT: B 1058 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7354 (mm-40) REVERT: B 1197 MET cc_start: 0.7975 (mtp) cc_final: 0.7535 (mpp) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.1790 time to fit residues: 110.6374 Evaluate side-chains 235 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 42 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 84 optimal weight: 0.0970 chunk 340 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 321 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 ASN A1000 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN C 653 ASN C 839 GLN B 219 HIS B 619 GLN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 GLN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 ASN B1147 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.052035 restraints weight = 137377.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053386 restraints weight = 82261.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.054289 restraints weight = 54908.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.054949 restraints weight = 40296.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055387 restraints weight = 31874.829| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30080 Z= 0.188 Angle : 0.718 16.738 41089 Z= 0.364 Chirality : 0.048 0.741 4790 Planarity : 0.005 0.075 5206 Dihedral : 7.358 128.744 5211 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3491 helix: 1.21 (0.18), residues: 835 sheet: 0.35 (0.18), residues: 755 loop : -0.55 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 280 TYR 0.026 0.002 TYR A 725 PHE 0.022 0.002 PHE C1113 TRP 0.027 0.002 TRP C 192 HIS 0.006 0.002 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00416 (29962) covalent geometry : angle 0.68861 (40798) SS BOND : bond 0.00548 ( 63) SS BOND : angle 1.20357 ( 126) hydrogen bonds : bond 0.04990 ( 1183) hydrogen bonds : angle 5.54246 ( 3345) link_BETA1-4 : bond 0.00540 ( 13) link_BETA1-4 : angle 1.90918 ( 39) link_NAG-ASN : bond 0.00638 ( 42) link_NAG-ASN : angle 3.48485 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.7936 (pt) cc_final: 0.7586 (pt) REVERT: A 194 MET cc_start: 0.5745 (tpt) cc_final: 0.4769 (tmm) REVERT: A 376 MET cc_start: 0.8174 (mtt) cc_final: 0.7885 (mmm) REVERT: A 679 MET cc_start: 0.7973 (mmm) cc_final: 0.7653 (mtt) REVERT: A 809 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8023 (p0) REVERT: A 916 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 961 LEU cc_start: 0.7183 (tp) cc_final: 0.6894 (tp) REVERT: A 1138 ASN cc_start: 0.8202 (m-40) cc_final: 0.7313 (p0) REVERT: A 1197 MET cc_start: 0.5564 (mmm) cc_final: 0.5304 (mmm) REVERT: C 47 VAL cc_start: 0.7687 (m) cc_final: 0.6980 (t) REVERT: C 58 ASP cc_start: 0.6596 (m-30) cc_final: 0.6323 (m-30) REVERT: C 82 MET cc_start: 0.7967 (mmm) cc_final: 0.7529 (mmm) REVERT: C 175 TYR cc_start: 0.7544 (m-80) cc_final: 0.7128 (m-80) REVERT: C 248 MET cc_start: 0.7698 (ppp) cc_final: 0.7344 (ppp) REVERT: C 346 GLU cc_start: 0.7729 (mp0) cc_final: 0.7320 (tm-30) REVERT: C 538 ASP cc_start: 0.6801 (m-30) cc_final: 0.5741 (p0) REVERT: C 724 ASN cc_start: 0.6000 (m110) cc_final: 0.5677 (m-40) REVERT: C 824 ASP cc_start: 0.8717 (t0) cc_final: 0.8366 (t0) REVERT: C 874 ASN cc_start: 0.7989 (t0) cc_final: 0.7749 (p0) REVERT: B 29 SER cc_start: 0.6868 (p) cc_final: 0.6588 (m) REVERT: B 32 ASN cc_start: 0.7462 (m110) cc_final: 0.6501 (t0) REVERT: B 82 MET cc_start: 0.7450 (mmm) cc_final: 0.7233 (tpp) REVERT: B 88 ASP cc_start: 0.6534 (t70) cc_final: 0.5978 (t0) REVERT: B 170 TYR cc_start: 0.4959 (m-80) cc_final: 0.4473 (m-80) REVERT: B 209 TYR cc_start: 0.7806 (p90) cc_final: 0.7310 (p90) REVERT: B 217 TYR cc_start: 0.6110 (m-80) cc_final: 0.5556 (m-80) REVERT: B 376 MET cc_start: 0.7053 (mtt) cc_final: 0.6763 (tpt) REVERT: B 383 SER cc_start: 0.7190 (t) cc_final: 0.6842 (p) REVERT: B 416 ASP cc_start: 0.7256 (m-30) cc_final: 0.6539 (m-30) REVERT: B 470 SER cc_start: 0.7660 (m) cc_final: 0.7389 (t) REVERT: B 542 PHE cc_start: 0.5145 (t80) cc_final: 0.4838 (t80) REVERT: B 656 GLN cc_start: 0.7859 (mt0) cc_final: 0.7118 (mt0) REVERT: B 669 PHE cc_start: 0.6267 (t80) cc_final: 0.6000 (t80) REVERT: B 812 GLU cc_start: 0.7395 (tp30) cc_final: 0.6631 (mt-10) REVERT: B 874 ASN cc_start: 0.7377 (t0) cc_final: 0.6805 (t0) REVERT: B 882 LEU cc_start: 0.7956 (mm) cc_final: 0.7704 (pp) REVERT: B 1005 THR cc_start: 0.7408 (m) cc_final: 0.6982 (p) REVERT: B 1006 MET cc_start: 0.7364 (tpp) cc_final: 0.6518 (tpp) REVERT: B 1197 MET cc_start: 0.8086 (mtp) cc_final: 0.7462 (mmm) outliers start: 2 outliers final: 1 residues processed: 328 average time/residue: 0.1703 time to fit residues: 93.8681 Evaluate side-chains 211 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 254 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 371 optimal weight: 40.0000 chunk 344 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 426 GLN A 705 ASN A 735 ASN A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 ASN C1147 GLN ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN B 705 ASN B 870 ASN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 GLN B1053 ASN B1141 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.050303 restraints weight = 139079.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.051597 restraints weight = 83288.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.052472 restraints weight = 55709.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.053130 restraints weight = 40699.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053524 restraints weight = 32288.528| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 30080 Z= 0.272 Angle : 0.811 14.479 41089 Z= 0.413 Chirality : 0.051 0.521 4790 Planarity : 0.006 0.074 5206 Dihedral : 7.829 121.071 5211 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3491 helix: 0.65 (0.18), residues: 827 sheet: 0.09 (0.18), residues: 757 loop : -0.95 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 454 TYR 0.044 0.003 TYR C 282 PHE 0.028 0.003 PHE B 980 TRP 0.022 0.002 TRP B 192 HIS 0.010 0.002 HIS A 532 Details of bonding type rmsd covalent geometry : bond 0.00614 (29962) covalent geometry : angle 0.78276 (40798) SS BOND : bond 0.00531 ( 63) SS BOND : angle 1.41145 ( 126) hydrogen bonds : bond 0.05531 ( 1183) hydrogen bonds : angle 5.87866 ( 3345) link_BETA1-4 : bond 0.00687 ( 13) link_BETA1-4 : angle 2.05123 ( 39) link_NAG-ASN : bond 0.00982 ( 42) link_NAG-ASN : angle 3.61285 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.8216 (mtt) cc_final: 0.7992 (mmm) REVERT: A 433 ASP cc_start: 0.8290 (t70) cc_final: 0.7880 (t0) REVERT: A 809 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7909 (p0) REVERT: A 916 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 961 LEU cc_start: 0.6919 (tp) cc_final: 0.6640 (tp) REVERT: A 1197 MET cc_start: 0.5758 (mmm) cc_final: 0.5518 (mmm) REVERT: C 58 ASP cc_start: 0.6799 (m-30) cc_final: 0.6289 (m-30) REVERT: C 82 MET cc_start: 0.7875 (mmm) cc_final: 0.7468 (mmm) REVERT: C 175 TYR cc_start: 0.7690 (m-80) cc_final: 0.7452 (m-80) REVERT: C 248 MET cc_start: 0.7812 (ppp) cc_final: 0.7359 (tmm) REVERT: C 299 MET cc_start: 0.7532 (ttm) cc_final: 0.7284 (ttm) REVERT: C 399 PHE cc_start: 0.6644 (m-10) cc_final: 0.6050 (m-80) REVERT: C 724 ASN cc_start: 0.6219 (m110) cc_final: 0.5912 (m-40) REVERT: C 824 ASP cc_start: 0.8839 (t0) cc_final: 0.8571 (t0) REVERT: C 898 VAL cc_start: 0.8249 (m) cc_final: 0.7934 (t) REVERT: C 938 THR cc_start: 0.7912 (p) cc_final: 0.7618 (t) REVERT: B 29 SER cc_start: 0.7025 (p) cc_final: 0.6774 (m) REVERT: B 32 ASN cc_start: 0.7631 (m110) cc_final: 0.6644 (t0) REVERT: B 66 LEU cc_start: 0.7618 (mp) cc_final: 0.7278 (mp) REVERT: B 209 TYR cc_start: 0.7980 (p90) cc_final: 0.7347 (p90) REVERT: B 217 TYR cc_start: 0.6321 (m-80) cc_final: 0.6042 (m-80) REVERT: B 283 LEU cc_start: 0.8834 (tt) cc_final: 0.8567 (tp) REVERT: B 376 MET cc_start: 0.6962 (mtt) cc_final: 0.6702 (tpt) REVERT: B 383 SER cc_start: 0.6708 (t) cc_final: 0.6326 (p) REVERT: B 470 SER cc_start: 0.7722 (m) cc_final: 0.7439 (t) REVERT: B 669 PHE cc_start: 0.6321 (t80) cc_final: 0.5924 (t80) REVERT: B 859 GLU cc_start: 0.8086 (pp20) cc_final: 0.7799 (tt0) REVERT: B 882 LEU cc_start: 0.7938 (mm) cc_final: 0.7566 (pp) REVERT: B 1005 THR cc_start: 0.7421 (m) cc_final: 0.6951 (p) REVERT: B 1182 ILE cc_start: 0.8474 (tp) cc_final: 0.8215 (tp) REVERT: B 1197 MET cc_start: 0.8202 (mtp) cc_final: 0.7724 (mmm) outliers start: 2 outliers final: 1 residues processed: 282 average time/residue: 0.1642 time to fit residues: 78.6056 Evaluate side-chains 191 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 346 optimal weight: 0.0670 chunk 227 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN A 809 ASN A 849 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN C 193 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN C 444 ASN C 735 ASN C 874 ASN C1147 GLN B 489 GLN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.052520 restraints weight = 136373.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.053761 restraints weight = 82225.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.054649 restraints weight = 55388.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055211 restraints weight = 40796.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055678 restraints weight = 32703.385| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30080 Z= 0.128 Angle : 0.643 15.429 41089 Z= 0.329 Chirality : 0.047 0.941 4790 Planarity : 0.005 0.063 5206 Dihedral : 7.106 125.007 5211 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 0.07 % Allowed : 1.33 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3491 helix: 1.04 (0.18), residues: 833 sheet: 0.10 (0.18), residues: 777 loop : -0.73 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1062 TYR 0.039 0.002 TYR B 282 PHE 0.027 0.002 PHE A 399 TRP 0.024 0.002 TRP C 192 HIS 0.007 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00280 (29962) covalent geometry : angle 0.61273 (40798) SS BOND : bond 0.00362 ( 63) SS BOND : angle 1.33049 ( 126) hydrogen bonds : bond 0.04594 ( 1183) hydrogen bonds : angle 5.36344 ( 3345) link_BETA1-4 : bond 0.00516 ( 13) link_BETA1-4 : angle 1.62858 ( 39) link_NAG-ASN : bond 0.00536 ( 42) link_NAG-ASN : angle 3.26812 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 THR cc_start: 0.7600 (t) cc_final: 0.7244 (m) REVERT: A 273 TRP cc_start: 0.6401 (m100) cc_final: 0.5874 (m100) REVERT: A 433 ASP cc_start: 0.8359 (t70) cc_final: 0.8080 (t70) REVERT: A 729 TYR cc_start: 0.7948 (t80) cc_final: 0.7725 (t80) REVERT: A 916 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 961 LEU cc_start: 0.6846 (tp) cc_final: 0.6473 (tp) REVERT: A 1197 MET cc_start: 0.5731 (mmm) cc_final: 0.5470 (mmm) REVERT: C 58 ASP cc_start: 0.6558 (m-30) cc_final: 0.6142 (m-30) REVERT: C 175 TYR cc_start: 0.7680 (m-80) cc_final: 0.7468 (m-80) REVERT: C 307 LYS cc_start: 0.7364 (tttm) cc_final: 0.7129 (mmtp) REVERT: C 348 TRP cc_start: 0.7170 (t60) cc_final: 0.6184 (t60) REVERT: C 399 PHE cc_start: 0.7091 (m-10) cc_final: 0.6830 (m-10) REVERT: C 538 ASP cc_start: 0.6805 (m-30) cc_final: 0.5884 (p0) REVERT: C 661 ASP cc_start: 0.6135 (t70) cc_final: 0.5931 (t70) REVERT: C 824 ASP cc_start: 0.8927 (t0) cc_final: 0.8615 (t0) REVERT: B 32 ASN cc_start: 0.7605 (m110) cc_final: 0.6448 (t0) REVERT: B 66 LEU cc_start: 0.7597 (mp) cc_final: 0.7157 (mp) REVERT: B 170 TYR cc_start: 0.5013 (m-80) cc_final: 0.4426 (m-80) REVERT: B 209 TYR cc_start: 0.7859 (p90) cc_final: 0.7310 (p90) REVERT: B 210 ASP cc_start: 0.6245 (t0) cc_final: 0.5999 (t0) REVERT: B 217 TYR cc_start: 0.6149 (m-80) cc_final: 0.5649 (m-80) REVERT: B 376 MET cc_start: 0.6842 (mtt) cc_final: 0.6549 (tpt) REVERT: B 383 SER cc_start: 0.6859 (t) cc_final: 0.6479 (p) REVERT: B 470 SER cc_start: 0.7768 (m) cc_final: 0.7517 (t) REVERT: B 542 PHE cc_start: 0.5065 (t80) cc_final: 0.4122 (t80) REVERT: B 656 GLN cc_start: 0.7781 (mt0) cc_final: 0.7292 (mt0) REVERT: B 669 PHE cc_start: 0.5996 (t80) cc_final: 0.5510 (t80) REVERT: B 812 GLU cc_start: 0.7224 (tp30) cc_final: 0.6403 (mt-10) REVERT: B 859 GLU cc_start: 0.7996 (pp20) cc_final: 0.7655 (tt0) REVERT: B 922 LYS cc_start: 0.7195 (mmtm) cc_final: 0.6917 (mmtm) REVERT: B 1005 THR cc_start: 0.7310 (m) cc_final: 0.6896 (p) REVERT: B 1108 SER cc_start: 0.8895 (t) cc_final: 0.8690 (p) REVERT: B 1197 MET cc_start: 0.8015 (mtp) cc_final: 0.7639 (mmm) outliers start: 2 outliers final: 0 residues processed: 301 average time/residue: 0.1696 time to fit residues: 86.4450 Evaluate side-chains 201 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 100 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 235 optimal weight: 0.0670 chunk 305 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 chunk 218 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 312 optimal weight: 1.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN C 735 ASN C 784 ASN C 874 ASN B 865 GLN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052668 restraints weight = 137865.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.054024 restraints weight = 84706.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054635 restraints weight = 55919.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.055069 restraints weight = 45089.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055438 restraints weight = 34781.160| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30080 Z= 0.125 Angle : 0.626 13.507 41089 Z= 0.319 Chirality : 0.045 0.614 4790 Planarity : 0.004 0.060 5206 Dihedral : 7.048 126.745 5211 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 0.07 % Allowed : 1.14 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3491 helix: 1.11 (0.18), residues: 833 sheet: 0.16 (0.18), residues: 777 loop : -0.72 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 280 TYR 0.031 0.002 TYR B 282 PHE 0.028 0.001 PHE A 399 TRP 0.023 0.001 TRP C 192 HIS 0.006 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00276 (29962) covalent geometry : angle 0.59933 (40798) SS BOND : bond 0.00420 ( 63) SS BOND : angle 1.19062 ( 126) hydrogen bonds : bond 0.04366 ( 1183) hydrogen bonds : angle 5.23754 ( 3345) link_BETA1-4 : bond 0.00454 ( 13) link_BETA1-4 : angle 1.55260 ( 39) link_NAG-ASN : bond 0.00564 ( 42) link_NAG-ASN : angle 3.05077 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 282 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6417 (m-80) cc_final: 0.6104 (m-80) REVERT: A 232 THR cc_start: 0.7581 (t) cc_final: 0.7246 (m) REVERT: A 248 MET cc_start: 0.7050 (mpp) cc_final: 0.6527 (mpp) REVERT: A 273 TRP cc_start: 0.6368 (m100) cc_final: 0.6060 (m100) REVERT: A 433 ASP cc_start: 0.8366 (t70) cc_final: 0.8098 (t70) REVERT: A 679 MET cc_start: 0.7211 (mtt) cc_final: 0.6733 (mtm) REVERT: A 726 PHE cc_start: 0.4904 (m-80) cc_final: 0.4017 (m-80) REVERT: A 729 TYR cc_start: 0.8049 (t80) cc_final: 0.7701 (t80) REVERT: A 916 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7296 (mt-10) REVERT: A 921 ASP cc_start: 0.7571 (m-30) cc_final: 0.7367 (t70) REVERT: A 961 LEU cc_start: 0.6717 (tp) cc_final: 0.6441 (tp) REVERT: A 1197 MET cc_start: 0.5577 (mmm) cc_final: 0.5332 (mmm) REVERT: C 58 ASP cc_start: 0.6281 (m-30) cc_final: 0.5918 (m-30) REVERT: C 82 MET cc_start: 0.7916 (mmm) cc_final: 0.7542 (mmm) REVERT: C 207 PHE cc_start: 0.7133 (m-80) cc_final: 0.6799 (m-10) REVERT: C 348 TRP cc_start: 0.7020 (t60) cc_final: 0.6300 (t60) REVERT: C 824 ASP cc_start: 0.8873 (t0) cc_final: 0.8574 (t0) REVERT: C 898 VAL cc_start: 0.8240 (m) cc_final: 0.7935 (t) REVERT: B 32 ASN cc_start: 0.7627 (m110) cc_final: 0.6599 (t0) REVERT: B 82 MET cc_start: 0.7310 (mmt) cc_final: 0.6875 (tpp) REVERT: B 209 TYR cc_start: 0.7860 (p90) cc_final: 0.7307 (p90) REVERT: B 210 ASP cc_start: 0.6032 (t0) cc_final: 0.5747 (t0) REVERT: B 217 TYR cc_start: 0.6224 (m-80) cc_final: 0.5699 (m-80) REVERT: B 376 MET cc_start: 0.6771 (mtt) cc_final: 0.6528 (tpt) REVERT: B 383 SER cc_start: 0.6872 (t) cc_final: 0.6532 (p) REVERT: B 470 SER cc_start: 0.7776 (m) cc_final: 0.7524 (t) REVERT: B 542 PHE cc_start: 0.5193 (t80) cc_final: 0.4198 (t80) REVERT: B 656 GLN cc_start: 0.7806 (mt0) cc_final: 0.7259 (mt0) REVERT: B 669 PHE cc_start: 0.6114 (t80) cc_final: 0.5601 (t80) REVERT: B 811 GLU cc_start: 0.5508 (pt0) cc_final: 0.5225 (pt0) REVERT: B 812 GLU cc_start: 0.7290 (tp30) cc_final: 0.6507 (mt-10) REVERT: B 859 GLU cc_start: 0.7965 (pp20) cc_final: 0.7638 (tt0) REVERT: B 1005 THR cc_start: 0.7376 (m) cc_final: 0.6961 (p) REVERT: B 1108 SER cc_start: 0.8931 (t) cc_final: 0.8703 (p) REVERT: B 1182 ILE cc_start: 0.8649 (tp) cc_final: 0.8430 (tp) REVERT: B 1197 MET cc_start: 0.8041 (mtp) cc_final: 0.7670 (mmm) outliers start: 2 outliers final: 1 residues processed: 284 average time/residue: 0.1652 time to fit residues: 80.5843 Evaluate side-chains 205 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 291 optimal weight: 0.0980 chunk 81 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 312 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 367 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN C 874 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.051852 restraints weight = 140365.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.053089 restraints weight = 85257.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053925 restraints weight = 57652.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054554 restraints weight = 42514.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.054893 restraints weight = 33754.927| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30080 Z= 0.162 Angle : 0.660 11.395 41089 Z= 0.337 Chirality : 0.048 1.019 4790 Planarity : 0.005 0.062 5206 Dihedral : 7.249 129.100 5211 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 0.07 % Allowed : 1.04 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3491 helix: 0.96 (0.18), residues: 832 sheet: 0.11 (0.18), residues: 796 loop : -0.82 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.035 0.002 TYR C 282 PHE 0.022 0.002 PHE B 980 TRP 0.019 0.002 TRP B 192 HIS 0.013 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00366 (29962) covalent geometry : angle 0.63485 (40798) SS BOND : bond 0.00428 ( 63) SS BOND : angle 1.32753 ( 126) hydrogen bonds : bond 0.04544 ( 1183) hydrogen bonds : angle 5.31818 ( 3345) link_BETA1-4 : bond 0.00498 ( 13) link_BETA1-4 : angle 1.66359 ( 39) link_NAG-ASN : bond 0.00435 ( 42) link_NAG-ASN : angle 2.97691 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 THR cc_start: 0.7565 (t) cc_final: 0.7203 (m) REVERT: A 248 MET cc_start: 0.7113 (mpp) cc_final: 0.6595 (mpp) REVERT: A 273 TRP cc_start: 0.6485 (m100) cc_final: 0.6122 (m100) REVERT: A 307 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7438 (mtpt) REVERT: A 433 ASP cc_start: 0.8359 (t70) cc_final: 0.8099 (t70) REVERT: A 679 MET cc_start: 0.7357 (mtt) cc_final: 0.6907 (mtm) REVERT: A 726 PHE cc_start: 0.4980 (m-80) cc_final: 0.3892 (m-80) REVERT: A 729 TYR cc_start: 0.7982 (t80) cc_final: 0.7690 (t80) REVERT: A 809 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.8032 (p0) REVERT: A 916 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7387 (mt-10) REVERT: A 961 LEU cc_start: 0.6749 (tp) cc_final: 0.6444 (tp) REVERT: A 1197 MET cc_start: 0.5674 (mmm) cc_final: 0.5420 (mmm) REVERT: C 58 ASP cc_start: 0.6532 (m-30) cc_final: 0.6096 (m-30) REVERT: C 82 MET cc_start: 0.7885 (mmm) cc_final: 0.7496 (mmm) REVERT: C 166 SER cc_start: 0.8441 (p) cc_final: 0.8221 (p) REVERT: C 175 TYR cc_start: 0.7592 (m-80) cc_final: 0.7387 (m-80) REVERT: C 207 PHE cc_start: 0.7214 (m-80) cc_final: 0.6948 (m-10) REVERT: C 348 TRP cc_start: 0.6842 (t60) cc_final: 0.6161 (t60) REVERT: C 824 ASP cc_start: 0.8856 (t0) cc_final: 0.8588 (t0) REVERT: C 898 VAL cc_start: 0.8269 (m) cc_final: 0.7971 (t) REVERT: C 938 THR cc_start: 0.8116 (p) cc_final: 0.7768 (t) REVERT: B 32 ASN cc_start: 0.7684 (m110) cc_final: 0.6593 (t0) REVERT: B 135 PHE cc_start: 0.7348 (m-80) cc_final: 0.7092 (m-10) REVERT: B 163 LEU cc_start: 0.8104 (tp) cc_final: 0.7873 (tp) REVERT: B 209 TYR cc_start: 0.7838 (p90) cc_final: 0.7194 (p90) REVERT: B 217 TYR cc_start: 0.6208 (m-80) cc_final: 0.5803 (m-80) REVERT: B 376 MET cc_start: 0.6948 (mtt) cc_final: 0.6708 (tpt) REVERT: B 383 SER cc_start: 0.6672 (t) cc_final: 0.6335 (p) REVERT: B 470 SER cc_start: 0.7774 (m) cc_final: 0.7533 (t) REVERT: B 542 PHE cc_start: 0.5133 (t80) cc_final: 0.4199 (t80) REVERT: B 543 THR cc_start: 0.6631 (m) cc_final: 0.6396 (m) REVERT: B 656 GLN cc_start: 0.7822 (mt0) cc_final: 0.7287 (mt0) REVERT: B 669 PHE cc_start: 0.6108 (t80) cc_final: 0.5623 (t80) REVERT: B 859 GLU cc_start: 0.8052 (pp20) cc_final: 0.7527 (tt0) REVERT: B 882 LEU cc_start: 0.7913 (mm) cc_final: 0.7667 (pp) REVERT: B 1005 THR cc_start: 0.7586 (m) cc_final: 0.7287 (p) REVERT: B 1182 ILE cc_start: 0.8619 (tp) cc_final: 0.8372 (tp) REVERT: B 1197 MET cc_start: 0.8026 (mtp) cc_final: 0.7753 (mmm) REVERT: B 1217 MET cc_start: 0.6918 (mpp) cc_final: 0.6630 (mpp) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.1662 time to fit residues: 79.5270 Evaluate side-chains 202 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 354 optimal weight: 40.0000 chunk 367 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 266 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 874 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.051343 restraints weight = 140454.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.052561 restraints weight = 85718.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053356 restraints weight = 58192.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.053993 restraints weight = 43235.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054339 restraints weight = 34607.088| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 30080 Z= 0.179 Angle : 0.690 11.046 41089 Z= 0.353 Chirality : 0.047 0.673 4790 Planarity : 0.005 0.063 5206 Dihedral : 7.505 132.377 5211 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3491 helix: 0.78 (0.18), residues: 841 sheet: 0.03 (0.18), residues: 779 loop : -0.93 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 280 TYR 0.036 0.002 TYR C 282 PHE 0.022 0.002 PHE C 103 TRP 0.026 0.002 TRP B 192 HIS 0.012 0.002 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00408 (29962) covalent geometry : angle 0.66462 (40798) SS BOND : bond 0.00440 ( 63) SS BOND : angle 1.42646 ( 126) hydrogen bonds : bond 0.04671 ( 1183) hydrogen bonds : angle 5.41280 ( 3345) link_BETA1-4 : bond 0.00512 ( 13) link_BETA1-4 : angle 1.68204 ( 39) link_NAG-ASN : bond 0.00595 ( 42) link_NAG-ASN : angle 3.05230 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 THR cc_start: 0.7559 (t) cc_final: 0.7202 (m) REVERT: A 248 MET cc_start: 0.7122 (mpp) cc_final: 0.6627 (mpp) REVERT: A 273 TRP cc_start: 0.6536 (m100) cc_final: 0.6150 (m100) REVERT: A 433 ASP cc_start: 0.8347 (t70) cc_final: 0.8130 (t70) REVERT: A 679 MET cc_start: 0.7493 (mtt) cc_final: 0.7204 (mtm) REVERT: A 726 PHE cc_start: 0.5096 (m-80) cc_final: 0.3972 (m-80) REVERT: A 809 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7959 (p0) REVERT: A 916 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7370 (mt-10) REVERT: A 1197 MET cc_start: 0.5700 (mmm) cc_final: 0.5448 (mmm) REVERT: C 58 ASP cc_start: 0.6499 (m-30) cc_final: 0.6036 (m-30) REVERT: C 82 MET cc_start: 0.8185 (mmm) cc_final: 0.7866 (mmm) REVERT: C 207 PHE cc_start: 0.7191 (m-80) cc_final: 0.6946 (m-10) REVERT: C 348 TRP cc_start: 0.6839 (t60) cc_final: 0.6395 (t60) REVERT: C 372 MET cc_start: 0.7014 (tpp) cc_final: 0.6646 (tpp) REVERT: C 824 ASP cc_start: 0.8942 (t0) cc_final: 0.8709 (t0) REVERT: C 898 VAL cc_start: 0.8169 (m) cc_final: 0.7857 (t) REVERT: C 938 THR cc_start: 0.8124 (p) cc_final: 0.7839 (t) REVERT: B 135 PHE cc_start: 0.7273 (m-80) cc_final: 0.6684 (m-80) REVERT: B 163 LEU cc_start: 0.7926 (tp) cc_final: 0.7698 (tp) REVERT: B 194 MET cc_start: 0.2921 (mtt) cc_final: 0.2696 (mtt) REVERT: B 209 TYR cc_start: 0.7851 (p90) cc_final: 0.7211 (p90) REVERT: B 217 TYR cc_start: 0.6338 (m-80) cc_final: 0.5754 (m-80) REVERT: B 376 MET cc_start: 0.6900 (mtt) cc_final: 0.6588 (tpt) REVERT: B 383 SER cc_start: 0.6670 (t) cc_final: 0.6366 (p) REVERT: B 470 SER cc_start: 0.7768 (m) cc_final: 0.7530 (t) REVERT: B 542 PHE cc_start: 0.4997 (t80) cc_final: 0.4043 (t80) REVERT: B 543 THR cc_start: 0.6707 (m) cc_final: 0.6421 (m) REVERT: B 564 LEU cc_start: 0.8309 (mt) cc_final: 0.7973 (mp) REVERT: B 656 GLN cc_start: 0.7881 (mt0) cc_final: 0.7452 (mt0) REVERT: B 669 PHE cc_start: 0.6142 (t80) cc_final: 0.5605 (t80) REVERT: B 812 GLU cc_start: 0.7281 (tp30) cc_final: 0.6521 (mt-10) REVERT: B 859 GLU cc_start: 0.8065 (pp20) cc_final: 0.7479 (tt0) REVERT: B 882 LEU cc_start: 0.7947 (mm) cc_final: 0.7672 (pp) REVERT: B 1005 THR cc_start: 0.7398 (m) cc_final: 0.6880 (p) REVERT: B 1108 SER cc_start: 0.8864 (t) cc_final: 0.8601 (p) REVERT: B 1197 MET cc_start: 0.8057 (mtp) cc_final: 0.7764 (mmm) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.1646 time to fit residues: 72.4856 Evaluate side-chains 189 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 330 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 335 optimal weight: 0.2980 chunk 80 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 598 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 ASN C 874 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050034 restraints weight = 142324.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.051183 restraints weight = 87380.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.052029 restraints weight = 59823.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.052525 restraints weight = 44532.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.052960 restraints weight = 36119.729| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.7084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 30080 Z= 0.273 Angle : 0.836 17.970 41089 Z= 0.424 Chirality : 0.052 0.644 4790 Planarity : 0.006 0.063 5206 Dihedral : 8.465 138.653 5211 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 0.03 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3491 helix: 0.23 (0.17), residues: 838 sheet: -0.37 (0.18), residues: 777 loop : -1.30 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 687 TYR 0.044 0.003 TYR C 282 PHE 0.038 0.003 PHE B 135 TRP 0.024 0.003 TRP B 192 HIS 0.016 0.002 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00623 (29962) covalent geometry : angle 0.80904 (40798) SS BOND : bond 0.00550 ( 63) SS BOND : angle 1.66078 ( 126) hydrogen bonds : bond 0.05453 ( 1183) hydrogen bonds : angle 5.90397 ( 3345) link_BETA1-4 : bond 0.00828 ( 13) link_BETA1-4 : angle 2.13742 ( 39) link_NAG-ASN : bond 0.00722 ( 42) link_NAG-ASN : angle 3.45883 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7155 (tt0) cc_final: 0.6885 (tt0) REVERT: A 433 ASP cc_start: 0.8334 (t70) cc_final: 0.8044 (t70) REVERT: A 679 MET cc_start: 0.7509 (mtt) cc_final: 0.7188 (mtm) REVERT: A 729 TYR cc_start: 0.8121 (t80) cc_final: 0.7919 (t80) REVERT: A 809 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7987 (p0) REVERT: A 916 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7432 (mt-10) REVERT: A 961 LEU cc_start: 0.6818 (tp) cc_final: 0.6588 (tp) REVERT: A 976 SER cc_start: 0.7763 (m) cc_final: 0.7339 (t) REVERT: C 58 ASP cc_start: 0.6666 (m-30) cc_final: 0.6100 (m-30) REVERT: C 361 GLU cc_start: 0.6698 (tt0) cc_final: 0.6221 (mt-10) REVERT: C 851 ASN cc_start: 0.7325 (m-40) cc_final: 0.6955 (m110) REVERT: C 898 VAL cc_start: 0.8257 (m) cc_final: 0.7940 (t) REVERT: B 82 MET cc_start: 0.7414 (mmt) cc_final: 0.6251 (mmt) REVERT: B 163 LEU cc_start: 0.8140 (tp) cc_final: 0.7823 (tp) REVERT: B 209 TYR cc_start: 0.7973 (p90) cc_final: 0.7290 (p90) REVERT: B 210 ASP cc_start: 0.6271 (t0) cc_final: 0.6002 (t0) REVERT: B 217 TYR cc_start: 0.6406 (m-80) cc_final: 0.5852 (m-80) REVERT: B 383 SER cc_start: 0.6548 (t) cc_final: 0.6235 (p) REVERT: B 656 GLN cc_start: 0.7606 (mt0) cc_final: 0.7380 (mt0) REVERT: B 669 PHE cc_start: 0.6087 (t80) cc_final: 0.5222 (t80) REVERT: B 882 LEU cc_start: 0.7827 (mm) cc_final: 0.7540 (pp) REVERT: B 1005 THR cc_start: 0.7606 (m) cc_final: 0.7331 (p) REVERT: B 1197 MET cc_start: 0.8158 (mtp) cc_final: 0.7872 (mmm) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1693 time to fit residues: 70.8042 Evaluate side-chains 177 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 190 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 809 ASN A1012 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN C 784 ASN C 874 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051863 restraints weight = 139855.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.053117 restraints weight = 84453.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053979 restraints weight = 56732.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.054511 restraints weight = 42023.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054969 restraints weight = 33945.819| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30080 Z= 0.133 Angle : 0.667 10.304 41089 Z= 0.340 Chirality : 0.046 0.601 4790 Planarity : 0.005 0.058 5206 Dihedral : 7.535 141.763 5211 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.76 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3491 helix: 0.73 (0.18), residues: 841 sheet: -0.20 (0.18), residues: 781 loop : -1.12 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 687 TYR 0.037 0.002 TYR C 282 PHE 0.035 0.002 PHE C 726 TRP 0.020 0.002 TRP A 273 HIS 0.013 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00295 (29962) covalent geometry : angle 0.64319 (40798) SS BOND : bond 0.00398 ( 63) SS BOND : angle 1.42241 ( 126) hydrogen bonds : bond 0.04514 ( 1183) hydrogen bonds : angle 5.41563 ( 3345) link_BETA1-4 : bond 0.00525 ( 13) link_BETA1-4 : angle 1.65585 ( 39) link_NAG-ASN : bond 0.00578 ( 42) link_NAG-ASN : angle 2.90711 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3921.41 seconds wall clock time: 69 minutes 23.92 seconds (4163.92 seconds total)