Starting phenix.real_space_refine on Sun Jul 5 19:38:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sb4_24969/07_2026/7sb4_24969.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sb4_24969/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7sb4_24969/07_2026/7sb4_24969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sb4_24969/07_2026/7sb4_24969.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sb4_24969/07_2026/7sb4_24969.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sb4_24969/07_2026/7sb4_24969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sb4_24969/07_2026/7sb4_24969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sb4_24969/07_2026/7sb4_24969.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 10 Time building chain proxies: 6.02, per 1000 atoms: 0.21 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 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: 1.29 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: 8.33 Time building geometry restraints manager: 2.88 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: 17218 34.94 - 69.88: 178 69.88 - 104.81: 19 104.81 - 139.75: 3 139.75 - 174.69: 2 Dihedral angle restraints: 17420 sinusoidal: 6483 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 17417 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: 2.720 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.500 Find NCS groups from input model: 1.030 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 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 : 10.745 174.688 10219 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/Z covalent geometry : bond 0.01968 / 1.06 (29962) covalent geometry : angle 1.78769 / 1.19 (40798) SS BOND : bond 0.04233 / 3.08 ( 63) SS BOND : angle 2.37868 / 1.62 ( 126) hydrogen bonds : bond 0.16615 / 11.12 ( 1183) hydrogen bonds : angle 8.39895 / 5.80 ( 3345) link_BETA1-4 : bond 0.06002 / 3.69 ( 13) link_BETA1-4 : angle 5.06170 / 3.28 ( 39) link_NAG-ASN : bond 0.06431 / 4.05 ( 42) link_NAG-ASN : angle 2.63197 / 1.66 ( 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 : 0.941 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: 0.1815 time to fit residues: 235.5931 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 : 1.116 ------------------------------------------------------------------------------- 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... A 344 ASN A 440 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.056593 restraints weight = 131572.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.057912 restraints weight = 79719.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.058828 restraints weight = 53483.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059464 restraints weight = 39215.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059869 restraints weight = 31126.909| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3075 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= 0.190 Angle : 0.798 16.996 41089 Z= 0.406 Chirality : 0.053 1.182 4790 Planarity : 0.005 0.049 5206 Dihedral : 7.859 161.701 4060 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3491 helix: 1.36 (0.18), residues: 833 sheet: 0.64 (0.18), residues: 721 loop : -0.02 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 912 TYR 0.027 0.002 TYR A 651 PHE 0.036 0.002 PHE C1113 TRP 0.028 0.003 TRP C 460 HIS 0.009 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (29962) covalent geometry : angle 0.76413 / 0.40 (40798) SS BOND : bond 0.00291 / 0.19 ( 63) SS BOND : angle 1.12296 / 0.73 ( 126) hydrogen bonds : bond 0.06180 / 4.08 ( 1183) hydrogen bonds : angle 6.21406 / 4.28 ( 3345) link_BETA1-4 : bond 0.00756 / 0.48 ( 13) link_BETA1-4 : angle 2.37306 / 1.71 ( 39) link_NAG-ASN : bond 0.00791 / 0.56 ( 42) link_NAG-ASN : angle 3.96811 / 2.42 ( 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 464 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 459 time to evaluate : 1.074 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: 0.6461 (mmm) cc_final: 0.6255 (mmm) REVERT: A 194 MET cc_start: 0.5516 (tpt) cc_final: 0.4106 (tmm) REVERT: A 254 TYR cc_start: 0.5176 (t80) cc_final: 0.4689 (t80) REVERT: A 263 ARG cc_start: 0.7132 (mmt180) cc_final: 0.6932 (tpt170) REVERT: A 277 LEU cc_start: 0.8037 (mt) cc_final: 0.7830 (mt) REVERT: A 376 MET cc_start: 0.6960 (mtm) cc_final: 0.6758 (mtt) REVERT: A 726 PHE cc_start: 0.3869 (m-10) cc_final: 0.3520 (m-80) REVERT: A 729 TYR cc_start: 0.7976 (t80) cc_final: 0.7668 (t80) REVERT: A 892 ASP cc_start: 0.5164 (t0) cc_final: 0.4724 (t0) REVERT: A 916 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 1063 PHE cc_start: 0.8567 (m-80) cc_final: 0.8325 (m-80) REVERT: A 1134 ASN cc_start: 0.9279 (m-40) cc_final: 0.9078 (m110) REVERT: A 1138 ASN cc_start: 0.7437 (m-40) cc_final: 0.6893 (p0) REVERT: A 1217 MET cc_start: 0.6164 (ptp) cc_final: 0.5898 (ptp) REVERT: C 60 VAL cc_start: 0.7883 (p) cc_final: 0.7659 (p) REVERT: C 170 TYR cc_start: 0.5229 (p90) cc_final: 0.4746 (p90) REVERT: C 258 LEU cc_start: 0.6853 (tp) cc_final: 0.6602 (tp) REVERT: C 280 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6567 (ttm-80) REVERT: C 346 GLU cc_start: 0.7143 (mp0) cc_final: 0.6738 (tm-30) REVERT: C 445 LEU cc_start: 0.7662 (mt) cc_final: 0.7402 (mt) REVERT: C 467 ILE cc_start: 0.7509 (mm) cc_final: 0.6758 (mm) REVERT: C 492 PHE cc_start: 0.6053 (m-80) cc_final: 0.5711 (m-10) REVERT: C 602 ASN cc_start: 0.7900 (t0) cc_final: 0.5442 (t0) REVERT: C 626 LYS cc_start: 0.8230 (mttp) cc_final: 0.7695 (mmmt) REVERT: C 824 ASP cc_start: 0.8600 (t0) cc_final: 0.8188 (t0) REVERT: C 868 VAL cc_start: 0.9036 (t) cc_final: 0.8683 (p) REVERT: C 965 ASN cc_start: 0.7020 (m-40) cc_final: 0.6622 (m110) REVERT: C 1002 LEU cc_start: 0.8531 (mt) cc_final: 0.7854 (tp) REVERT: C 1005 THR cc_start: 0.8293 (t) cc_final: 0.8047 (m) REVERT: C 1197 MET cc_start: 0.6638 (mtp) cc_final: 0.5934 (mtp) REVERT: B 66 LEU cc_start: 0.7775 (mp) cc_final: 0.7503 (mp) REVERT: B 82 MET cc_start: 0.7083 (mmm) cc_final: 0.6683 (tpp) REVERT: B 163 LEU cc_start: 0.8054 (tp) cc_final: 0.7757 (tp) REVERT: B 170 TYR cc_start: 0.5355 (m-80) cc_final: 0.4947 (m-80) REVERT: B 172 MET cc_start: 0.7411 (mtp) cc_final: 0.7110 (mtm) REVERT: B 194 MET cc_start: 0.4109 (ttm) cc_final: 0.3755 (mtp) REVERT: B 209 TYR cc_start: 0.7754 (p90) cc_final: 0.7352 (p90) REVERT: B 217 TYR cc_start: 0.6091 (m-80) cc_final: 0.5416 (m-80) REVERT: B 287 ASN cc_start: 0.6154 (t0) cc_final: 0.5897 (m-40) REVERT: B 372 MET cc_start: 0.6856 (tpp) cc_final: 0.6408 (tpp) REVERT: B 383 SER cc_start: 0.7223 (t) cc_final: 0.6919 (p) REVERT: B 589 ASP cc_start: 0.5879 (t0) cc_final: 0.5585 (m-30) REVERT: B 669 PHE cc_start: 0.6111 (t80) cc_final: 0.5729 (t80) REVERT: B 812 GLU cc_start: 0.7266 (tp30) cc_final: 0.6563 (mt-10) REVERT: B 846 PHE cc_start: 0.8391 (m-80) cc_final: 0.7880 (m-80) REVERT: B 848 ASP cc_start: 0.6579 (m-30) cc_final: 0.6356 (m-30) REVERT: B 862 ASP cc_start: 0.7246 (t0) cc_final: 0.6224 (t70) REVERT: B 874 ASN cc_start: 0.7115 (t0) cc_final: 0.6532 (t0) REVERT: B 882 LEU cc_start: 0.7744 (mt) cc_final: 0.7385 (mt) REVERT: B 998 ARG cc_start: 0.7395 (mmm160) cc_final: 0.6925 (tpp-160) REVERT: B 1005 THR cc_start: 0.7746 (m) cc_final: 0.7331 (m) REVERT: B 1135 PHE cc_start: 0.8330 (t80) cc_final: 0.8106 (t80) REVERT: B 1197 MET cc_start: 0.7911 (mtp) cc_final: 0.7139 (mmm) outliers start: 5 outliers final: 1 residues processed: 464 average time/residue: 0.1708 time to fit residues: 130.7666 Evaluate side-chains 252 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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: 5.9990 chunk 197 optimal weight: 4.9990 chunk 321 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 187 HIS A 219 HIS A 426 GLN A 444 ASN A 641 GLN A 849 ASN A1012 ASN A1103 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN B 160 GLN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 HIS B 219 HIS B 281 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 GLN B1028 GLN B1071 GLN B1091 ASN ** B1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.051616 restraints weight = 138482.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.053000 restraints weight = 81480.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053974 restraints weight = 53756.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054563 restraints weight = 39082.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.055061 restraints weight = 31258.853| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 30080 Z= 0.253 Angle : 0.829 15.346 41089 Z= 0.421 Chirality : 0.051 0.591 4790 Planarity : 0.006 0.064 5206 Dihedral : 7.275 123.884 4060 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 0.16 % Allowed : 2.86 % Favored : 96.97 % 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: 0.97 (0.18), residues: 834 sheet: 0.40 (0.18), residues: 773 loop : -0.46 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 431 TYR 0.029 0.003 TYR A 254 PHE 0.028 0.003 PHE A 399 TRP 0.027 0.003 TRP B 586 HIS 0.008 0.002 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 (29962) covalent geometry : angle 0.80390 / 0.42 (40798) SS BOND : bond 0.00887 / 0.49 ( 63) SS BOND : angle 1.30722 / 0.81 ( 126) hydrogen bonds : bond 0.05778 / 3.77 ( 1183) hydrogen bonds : angle 5.90804 / 4.04 ( 3345) link_BETA1-4 : bond 0.00750 / 0.36 ( 13) link_BETA1-4 : angle 1.85215 / 1.26 ( 39) link_NAG-ASN : bond 0.00764 / 0.54 ( 42) link_NAG-ASN : angle 3.50535 / 2.15 ( 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 348 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 343 time to evaluate : 1.150 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: 0.6810 (mmm) cc_final: 0.6574 (mmm) REVERT: A 194 MET cc_start: 0.5680 (tpt) cc_final: 0.4671 (tmm) REVERT: A 307 LYS cc_start: 0.7354 (mttt) cc_final: 0.7115 (mtmt) REVERT: A 376 MET cc_start: 0.7618 (mtm) cc_final: 0.7417 (mtt) REVERT: A 599 ILE cc_start: 0.7827 (mt) cc_final: 0.7505 (mt) REVERT: A 679 MET cc_start: 0.7899 (mmm) cc_final: 0.7569 (mtt) REVERT: A 729 TYR cc_start: 0.7836 (t80) cc_final: 0.7601 (t80) REVERT: A 916 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 961 LEU cc_start: 0.7326 (tp) cc_final: 0.6974 (tp) REVERT: A 1138 ASN cc_start: 0.8136 (m-40) cc_final: 0.7269 (p0) REVERT: A 1197 MET cc_start: 0.5756 (mmm) cc_final: 0.5543 (mmm) REVERT: C 271 GLU cc_start: 0.5330 (mt-10) cc_final: 0.4699 (mp0) REVERT: C 280 ARG cc_start: 0.6644 (mtp85) cc_final: 0.6328 (mmt90) REVERT: C 299 MET cc_start: 0.7314 (ttm) cc_final: 0.7099 (ttm) REVERT: C 346 GLU cc_start: 0.7705 (mp0) cc_final: 0.7225 (tm-30) REVERT: C 538 ASP cc_start: 0.6910 (m-30) cc_final: 0.5808 (p0) REVERT: C 646 GLU cc_start: 0.7030 (tp30) cc_final: 0.6427 (tm-30) REVERT: C 824 ASP cc_start: 0.8715 (t0) cc_final: 0.8370 (t0) REVERT: C 874 ASN cc_start: 0.7789 (t0) cc_final: 0.7534 (p0) REVERT: C 898 VAL cc_start: 0.8475 (m) cc_final: 0.8165 (t) REVERT: C 1002 LEU cc_start: 0.8418 (mt) cc_final: 0.8041 (tp) REVERT: C 1197 MET cc_start: 0.6871 (mtp) cc_final: 0.6176 (mtt) REVERT: B 29 SER cc_start: 0.6859 (p) cc_final: 0.6551 (m) REVERT: B 32 ASN cc_start: 0.7762 (m110) cc_final: 0.6574 (t0) REVERT: B 88 ASP cc_start: 0.6703 (t70) cc_final: 0.5787 (t0) REVERT: B 170 TYR cc_start: 0.4599 (m-80) cc_final: 0.3625 (m-80) REVERT: B 209 TYR cc_start: 0.8240 (p90) cc_final: 0.7748 (p90) REVERT: B 217 TYR cc_start: 0.6292 (m-80) cc_final: 0.5745 (m-80) REVERT: B 369 ASN cc_start: 0.6974 (m-40) cc_final: 0.6638 (m-40) REVERT: B 383 SER cc_start: 0.7396 (t) cc_final: 0.7127 (p) REVERT: B 470 SER cc_start: 0.7601 (m) cc_final: 0.7311 (t) REVERT: B 542 PHE cc_start: 0.5229 (t80) cc_final: 0.4904 (t80) REVERT: B 656 GLN cc_start: 0.8174 (mt0) cc_final: 0.7673 (mt0) REVERT: B 669 PHE cc_start: 0.6366 (t80) cc_final: 0.5735 (t80) REVERT: B 717 ILE cc_start: 0.7658 (mm) cc_final: 0.7424 (pt) REVERT: B 812 GLU cc_start: 0.7361 (tp30) cc_final: 0.6474 (mt-10) REVERT: B 874 ASN cc_start: 0.7356 (t0) cc_final: 0.6784 (t0) REVERT: B 998 ARG cc_start: 0.7274 (mmm160) cc_final: 0.6843 (tpp-160) REVERT: B 1005 THR cc_start: 0.7417 (m) cc_final: 0.6902 (p) REVERT: B 1197 MET cc_start: 0.8110 (mtp) cc_final: 0.7599 (mpp) REVERT: B 1217 MET cc_start: 0.7240 (mpp) cc_final: 0.7026 (mpp) outliers start: 5 outliers final: 1 residues processed: 345 average time/residue: 0.1594 time to fit residues: 91.9517 Evaluate side-chains 217 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 10.0000 chunk 269 optimal weight: 6.9990 chunk 88 optimal weight: 0.0570 chunk 238 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 340 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 641 GLN A 705 ASN A 809 ASN A 849 ASN A1000 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN ** C1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 619 GLN B 705 ASN B 865 GLN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 ASN B1085 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.052218 restraints weight = 137843.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.053483 restraints weight = 83680.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054335 restraints weight = 56707.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.054969 restraints weight = 42098.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055334 restraints weight = 33710.663| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 30080 Z= 0.171 Angle : 0.692 13.118 41089 Z= 0.351 Chirality : 0.046 0.406 4790 Planarity : 0.005 0.064 5206 Dihedral : 6.517 123.154 4060 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % 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: 0.02 (0.14), residues: 3491 helix: 1.10 (0.18), residues: 834 sheet: 0.36 (0.18), residues: 759 loop : -0.60 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1062 TYR 0.036 0.002 TYR C 282 PHE 0.024 0.002 PHE B 895 TRP 0.020 0.002 TRP C 192 HIS 0.006 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (29962) covalent geometry : angle 0.66608 / 0.35 (40798) SS BOND : bond 0.00414 / 0.26 ( 63) SS BOND : angle 1.21698 / 0.73 ( 126) hydrogen bonds : bond 0.04929 / 3.21 ( 1183) hydrogen bonds : angle 5.52301 / 3.80 ( 3345) link_BETA1-4 : bond 0.00455 / 0.26 ( 13) link_BETA1-4 : angle 1.54542 / 1.11 ( 39) link_NAG-ASN : bond 0.00799 / 0.39 ( 42) link_NAG-ASN : angle 3.17709 / 1.95 ( 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 319 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 0.887 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 26 ARG cc_start: 0.6385 (mtm180) cc_final: 0.5988 (mtm180) REVERT: A 194 MET cc_start: 0.5759 (tpt) cc_final: 0.4821 (tmm) REVERT: A 307 LYS cc_start: 0.7352 (mttt) cc_final: 0.7114 (mtmt) REVERT: A 433 ASP cc_start: 0.8391 (t70) cc_final: 0.8120 (t0) REVERT: A 599 ILE cc_start: 0.7737 (mt) cc_final: 0.7480 (mt) REVERT: A 679 MET cc_start: 0.7951 (mmm) cc_final: 0.7603 (mtt) REVERT: A 729 TYR cc_start: 0.7888 (t80) cc_final: 0.7585 (t80) REVERT: A 916 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 961 LEU cc_start: 0.6880 (tp) cc_final: 0.6521 (tp) REVERT: A 1138 ASN cc_start: 0.8156 (m-40) cc_final: 0.7372 (p0) REVERT: C 54 TYR cc_start: 0.6703 (p90) cc_final: 0.5972 (p90) REVERT: C 58 ASP cc_start: 0.6517 (m-30) cc_final: 0.6147 (m-30) REVERT: C 299 MET cc_start: 0.7387 (ttm) cc_final: 0.6654 (ttm) REVERT: C 307 LYS cc_start: 0.7447 (tttt) cc_final: 0.7205 (tttm) REVERT: C 346 GLU cc_start: 0.7702 (mp0) cc_final: 0.7307 (tm-30) REVERT: C 348 TRP cc_start: 0.7244 (t60) cc_final: 0.6244 (t60) REVERT: C 538 ASP cc_start: 0.6737 (m-30) cc_final: 0.5694 (p0) REVERT: C 596 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7601 (mmtp) REVERT: C 724 ASN cc_start: 0.6068 (m110) cc_final: 0.5811 (m-40) REVERT: C 824 ASP cc_start: 0.8789 (t0) cc_final: 0.8422 (t0) REVERT: C 874 ASN cc_start: 0.7372 (t0) cc_final: 0.6985 (t0) REVERT: C 1197 MET cc_start: 0.6657 (mtp) cc_final: 0.5891 (mtm) REVERT: B 29 SER cc_start: 0.6893 (p) cc_final: 0.6548 (m) REVERT: B 32 ASN cc_start: 0.7592 (m110) cc_final: 0.6572 (t0) REVERT: B 170 TYR cc_start: 0.4763 (m-80) cc_final: 0.4044 (m-80) REVERT: B 209 TYR cc_start: 0.8108 (p90) cc_final: 0.7526 (p90) REVERT: B 217 TYR cc_start: 0.6077 (m-80) cc_final: 0.5521 (m-80) REVERT: B 296 VAL cc_start: 0.8609 (t) cc_final: 0.8214 (t) REVERT: B 376 MET cc_start: 0.6975 (mtt) cc_final: 0.6625 (tpt) REVERT: B 383 SER cc_start: 0.7327 (t) cc_final: 0.6987 (p) REVERT: B 416 ASP cc_start: 0.7098 (m-30) cc_final: 0.6490 (m-30) REVERT: B 470 SER cc_start: 0.7723 (m) cc_final: 0.7416 (t) REVERT: B 542 PHE cc_start: 0.4843 (t80) cc_final: 0.4585 (t80) REVERT: B 656 GLN cc_start: 0.7883 (mt0) cc_final: 0.7074 (mt0) REVERT: B 717 ILE cc_start: 0.7641 (mm) cc_final: 0.7385 (pt) REVERT: B 812 GLU cc_start: 0.7359 (tp30) cc_final: 0.6456 (mt-10) REVERT: B 848 ASP cc_start: 0.5898 (m-30) cc_final: 0.5666 (m-30) REVERT: B 874 ASN cc_start: 0.7369 (t0) cc_final: 0.6955 (t0) REVERT: B 882 LEU cc_start: 0.7976 (mm) cc_final: 0.7668 (pp) REVERT: B 1005 THR cc_start: 0.7322 (m) cc_final: 0.6888 (p) REVERT: B 1006 MET cc_start: 0.7390 (tpp) cc_final: 0.6572 (tpp) REVERT: B 1197 MET cc_start: 0.7981 (mtp) cc_final: 0.7418 (mmm) outliers start: 1 outliers final: 1 residues processed: 319 average time/residue: 0.1741 time to fit residues: 92.9092 Evaluate side-chains 218 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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: 10.0000 chunk 60 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 182 optimal weight: 8.9990 chunk 371 optimal weight: 40.0000 chunk 344 optimal weight: 10.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 735 ASN A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 GLN ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1147 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 = 0.3104 r_free = 0.3104 target = 0.059718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.050459 restraints weight = 140550.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.051711 restraints weight = 89370.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052535 restraints weight = 57678.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.052812 restraints weight = 46995.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.053136 restraints weight = 37047.638| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.253 30080 Z= 0.271 Angle : 0.839 11.177 41089 Z= 0.425 Chirality : 0.052 0.515 4790 Planarity : 0.006 0.058 5206 Dihedral : 6.865 121.308 4060 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.01 % 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: -0.66 (0.13), residues: 3491 helix: 0.56 (0.18), residues: 827 sheet: 0.04 (0.18), residues: 752 loop : -1.08 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1062 TYR 0.032 0.003 TYR C 282 PHE 0.032 0.003 PHE A 399 TRP 0.038 0.003 TRP A 273 HIS 0.009 0.002 HIS B1157 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.27 (29962) covalent geometry : angle 0.81722 / 0.42 (40798) SS BOND : bond 0.00728 / 0.46 ( 63) SS BOND : angle 1.38969 / 0.87 ( 126) hydrogen bonds : bond 0.05725 / 3.74 ( 1183) hydrogen bonds : angle 5.92606 / 4.07 ( 3345) link_BETA1-4 : bond 0.00702 / 0.36 ( 13) link_BETA1-4 : angle 1.92479 / 1.25 ( 39) link_NAG-ASN : bond 0.01054 / 0.53 ( 42) link_NAG-ASN : angle 3.21240 / 2.09 ( 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 271 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 1.111 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 174 GLU cc_start: 0.7340 (tt0) cc_final: 0.6990 (tt0) REVERT: A 273 TRP cc_start: 0.6203 (m100) cc_final: 0.5819 (m100) REVERT: A 433 ASP cc_start: 0.8322 (t70) cc_final: 0.7983 (t0) REVERT: A 599 ILE cc_start: 0.8057 (mt) cc_final: 0.7827 (mt) REVERT: A 809 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7994 (p0) REVERT: A 916 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7544 (mt-10) REVERT: A 944 ARG cc_start: 0.8495 (mmt90) cc_final: 0.8004 (ttm-80) REVERT: A 961 LEU cc_start: 0.6666 (tp) cc_final: 0.6329 (tp) REVERT: C 58 ASP cc_start: 0.6489 (m-30) cc_final: 0.6022 (m-30) REVERT: C 164 GLU cc_start: 0.5748 (pt0) cc_final: 0.5516 (pm20) REVERT: C 307 LYS cc_start: 0.7521 (tttt) cc_final: 0.7286 (tttm) REVERT: C 596 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7723 (mttp) REVERT: C 824 ASP cc_start: 0.9045 (t0) cc_final: 0.8796 (t0) REVERT: C 938 THR cc_start: 0.7923 (p) cc_final: 0.7670 (t) REVERT: B 29 SER cc_start: 0.7138 (p) cc_final: 0.6925 (m) REVERT: B 88 ASP cc_start: 0.6818 (t70) cc_final: 0.6415 (t0) REVERT: B 209 TYR cc_start: 0.8239 (p90) cc_final: 0.7565 (p90) REVERT: B 217 TYR cc_start: 0.6236 (m-80) cc_final: 0.6028 (m-80) REVERT: B 376 MET cc_start: 0.6880 (mtt) cc_final: 0.6603 (tpt) REVERT: B 383 SER cc_start: 0.6623 (t) cc_final: 0.6346 (p) REVERT: B 470 SER cc_start: 0.7728 (m) cc_final: 0.7475 (t) REVERT: B 669 PHE cc_start: 0.5785 (t80) cc_final: 0.5489 (t80) REVERT: B 859 GLU cc_start: 0.8101 (pp20) cc_final: 0.7649 (tt0) REVERT: B 882 LEU cc_start: 0.7769 (mm) cc_final: 0.7497 (pp) REVERT: B 1005 THR cc_start: 0.7549 (m) cc_final: 0.7261 (p) REVERT: B 1182 ILE cc_start: 0.8366 (tp) cc_final: 0.8091 (tp) REVERT: B 1197 MET cc_start: 0.8127 (mtp) cc_final: 0.7688 (mmm) outliers start: 2 outliers final: 0 residues processed: 270 average time/residue: 0.1732 time to fit residues: 78.8648 Evaluate side-chains 187 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 0.0020 chunk 227 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 89 optimal weight: 0.0470 chunk 136 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 ASN B 489 GLN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS 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 = 0.060689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.050695 restraints weight = 139045.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052168 restraints weight = 79742.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.053134 restraints weight = 51736.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.053858 restraints weight = 37204.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.054320 restraints weight = 28833.170| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 30080 Z= 0.173 Angle : 0.697 11.626 41089 Z= 0.354 Chirality : 0.046 0.412 4790 Planarity : 0.005 0.049 5206 Dihedral : 6.533 127.455 4060 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 0.03 % Allowed : 1.69 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3491 helix: 0.76 (0.18), residues: 836 sheet: 0.05 (0.18), residues: 757 loop : -0.99 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.036 0.002 TYR C 282 PHE 0.019 0.002 PHE B 980 TRP 0.023 0.002 TRP B 192 HIS 0.007 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (29962) covalent geometry : angle 0.67028 / 0.35 (40798) SS BOND : bond 0.00471 / 0.31 ( 63) SS BOND : angle 1.63571 / 1.43 ( 126) hydrogen bonds : bond 0.04922 / 3.19 ( 1183) hydrogen bonds : angle 5.58768 / 3.86 ( 3345) link_BETA1-4 : bond 0.00534 / 0.31 ( 13) link_BETA1-4 : angle 1.56107 / 1.11 ( 39) link_NAG-ASN : bond 0.00619 / 0.38 ( 42) link_NAG-ASN : angle 3.05520 / 2.02 ( 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 279 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 1.034 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: 0.7723 (t) cc_final: 0.7315 (m) REVERT: A 307 LYS cc_start: 0.7304 (mttt) cc_final: 0.7085 (mtmt) REVERT: A 433 ASP cc_start: 0.8384 (t70) cc_final: 0.8095 (t70) REVERT: A 599 ILE cc_start: 0.8027 (mt) cc_final: 0.7819 (mt) REVERT: A 809 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8156 (p0) REVERT: A 916 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7315 (mt-10) REVERT: C 58 ASP cc_start: 0.6419 (m-30) cc_final: 0.5982 (m-30) REVERT: C 256 MET cc_start: 0.6213 (mmm) cc_final: 0.5943 (mmt) REVERT: C 307 LYS cc_start: 0.7588 (tttt) cc_final: 0.7326 (tttm) REVERT: C 399 PHE cc_start: 0.7132 (m-10) cc_final: 0.6889 (m-80) REVERT: C 538 ASP cc_start: 0.6892 (m-30) cc_final: 0.5740 (p0) REVERT: C 824 ASP cc_start: 0.9031 (t0) cc_final: 0.8744 (t0) REVERT: C 898 VAL cc_start: 0.8305 (m) cc_final: 0.8097 (t) REVERT: C 938 THR cc_start: 0.7924 (p) cc_final: 0.7589 (t) REVERT: B 32 ASN cc_start: 0.7773 (m110) cc_final: 0.6756 (t0) REVERT: B 170 TYR cc_start: 0.4792 (m-80) cc_final: 0.4523 (m-80) REVERT: B 209 TYR cc_start: 0.8215 (p90) cc_final: 0.7533 (p90) REVERT: B 376 MET cc_start: 0.6818 (mtt) cc_final: 0.6574 (tpt) REVERT: B 383 SER cc_start: 0.6803 (t) cc_final: 0.6402 (p) REVERT: B 470 SER cc_start: 0.7766 (m) cc_final: 0.7484 (t) REVERT: B 656 GLN cc_start: 0.7737 (mt0) cc_final: 0.7287 (mt0) REVERT: B 669 PHE cc_start: 0.5854 (t80) cc_final: 0.5609 (t80) REVERT: B 859 GLU cc_start: 0.8039 (pp20) cc_final: 0.7612 (tt0) REVERT: B 882 LEU cc_start: 0.7891 (mm) cc_final: 0.7640 (pp) REVERT: B 1005 THR cc_start: 0.7488 (m) cc_final: 0.7111 (p) REVERT: B 1006 MET cc_start: 0.7587 (tpt) cc_final: 0.7194 (mmm) REVERT: B 1182 ILE cc_start: 0.8464 (tp) cc_final: 0.8143 (tp) REVERT: B 1197 MET cc_start: 0.8090 (mtp) cc_final: 0.7647 (mmm) REVERT: B 1217 MET cc_start: 0.7279 (mpp) cc_final: 0.7044 (mpp) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.1742 time to fit residues: 81.4449 Evaluate side-chains 195 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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: 8.9990 chunk 159 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 235 optimal weight: 0.0670 chunk 305 optimal weight: 0.9990 chunk 314 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 312 optimal weight: 0.0370 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 ASN C 870 ASN C 874 ASN C1021 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 HIS ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.061916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052060 restraints weight = 137659.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053482 restraints weight = 79890.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054499 restraints weight = 52294.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.055127 restraints weight = 37480.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055648 restraints weight = 29371.243| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30080 Z= 0.123 Angle : 0.631 11.593 41089 Z= 0.323 Chirality : 0.044 0.326 4790 Planarity : 0.004 0.052 5206 Dihedral : 6.239 130.080 4060 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.85 % 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: -0.32 (0.14), residues: 3491 helix: 1.03 (0.18), residues: 842 sheet: 0.06 (0.18), residues: 745 loop : -0.88 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 944 TYR 0.036 0.002 TYR C 282 PHE 0.030 0.001 PHE A 399 TRP 0.018 0.002 TRP C 192 HIS 0.012 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (29962) covalent geometry : angle 0.61126 / 0.32 (40798) SS BOND : bond 0.00361 / 0.21 ( 63) SS BOND : angle 1.19336 / 0.93 ( 126) hydrogen bonds : bond 0.04464 / 2.88 ( 1183) hydrogen bonds : angle 5.29241 / 3.65 ( 3345) link_BETA1-4 : bond 0.00460 / 0.27 ( 13) link_BETA1-4 : angle 1.37727 / 0.97 ( 39) link_NAG-ASN : bond 0.00496 / 0.28 ( 42) link_NAG-ASN : angle 2.63421 / 1.67 ( 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 278 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 1.036 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: 0.7360 (t) cc_final: 0.6913 (m) REVERT: A 248 MET cc_start: 0.7262 (mpp) cc_final: 0.6813 (mpp) REVERT: A 299 MET cc_start: 0.7927 (mmt) cc_final: 0.7651 (mmt) REVERT: A 433 ASP cc_start: 0.8403 (t70) cc_final: 0.8149 (t70) REVERT: A 679 MET cc_start: 0.7789 (mtt) cc_final: 0.7120 (mtm) REVERT: A 916 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7225 (mt-10) REVERT: A 921 ASP cc_start: 0.7775 (m-30) cc_final: 0.7535 (t70) REVERT: A 961 LEU cc_start: 0.7054 (tp) cc_final: 0.6750 (tp) REVERT: A 1197 MET cc_start: 0.5638 (mmm) cc_final: 0.5424 (mmm) REVERT: C 58 ASP cc_start: 0.6722 (m-30) cc_final: 0.6256 (m-30) REVERT: C 348 TRP cc_start: 0.7009 (t60) cc_final: 0.6504 (t60) REVERT: C 824 ASP cc_start: 0.8894 (t0) cc_final: 0.8584 (t0) REVERT: C 938 THR cc_start: 0.7926 (p) cc_final: 0.7564 (t) REVERT: B 32 ASN cc_start: 0.7801 (m110) cc_final: 0.6865 (t0) REVERT: B 122 MET cc_start: 0.7468 (tpp) cc_final: 0.7149 (tpt) REVERT: B 209 TYR cc_start: 0.8085 (p90) cc_final: 0.7411 (p90) REVERT: B 217 TYR cc_start: 0.5980 (m-10) cc_final: 0.5767 (m-80) REVERT: B 376 MET cc_start: 0.6817 (mtt) cc_final: 0.6593 (tpt) REVERT: B 383 SER cc_start: 0.6962 (t) cc_final: 0.6507 (p) REVERT: B 470 SER cc_start: 0.7755 (m) cc_final: 0.7477 (t) REVERT: B 656 GLN cc_start: 0.7811 (mt0) cc_final: 0.7370 (mt0) REVERT: B 859 GLU cc_start: 0.8035 (pp20) cc_final: 0.7676 (tt0) REVERT: B 1005 THR cc_start: 0.7473 (m) cc_final: 0.6878 (p) REVERT: B 1182 ILE cc_start: 0.8608 (tp) cc_final: 0.8302 (tp) REVERT: B 1197 MET cc_start: 0.8274 (mtp) cc_final: 0.7786 (mmm) REVERT: B 1229 TYR cc_start: 0.7634 (t80) cc_final: 0.7429 (t80) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.1615 time to fit residues: 76.4999 Evaluate side-chains 189 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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: 0.9980 chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 344 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 312 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 367 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.051842 restraints weight = 139078.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.053198 restraints weight = 81808.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.054146 restraints weight = 53803.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054758 restraints weight = 38993.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055226 restraints weight = 30742.425| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30080 Z= 0.141 Angle : 0.638 12.725 41089 Z= 0.326 Chirality : 0.045 0.302 4790 Planarity : 0.004 0.053 5206 Dihedral : 6.244 131.217 4060 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 0.07 % Allowed : 0.91 % Favored : 99.02 % 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: -0.35 (0.14), residues: 3491 helix: 1.01 (0.18), residues: 844 sheet: 0.06 (0.18), residues: 743 loop : -0.92 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 944 TYR 0.029 0.002 TYR C 282 PHE 0.033 0.002 PHE A 399 TRP 0.016 0.002 TRP C 192 HIS 0.009 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (29962) covalent geometry : angle 0.61910 / 0.32 (40798) SS BOND : bond 0.00346 / 0.19 ( 63) SS BOND : angle 1.25355 / 0.94 ( 126) hydrogen bonds : bond 0.04416 / 2.86 ( 1183) hydrogen bonds : angle 5.26678 / 3.62 ( 3345) link_BETA1-4 : bond 0.00372 / 0.21 ( 13) link_BETA1-4 : angle 1.40887 / 0.97 ( 39) link_NAG-ASN : bond 0.00495 / 0.30 ( 42) link_NAG-ASN : angle 2.57447 / 1.62 ( 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 261 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6461 (m-80) cc_final: 0.6104 (m-80) REVERT: A 232 THR cc_start: 0.7454 (t) cc_final: 0.7172 (m) REVERT: A 248 MET cc_start: 0.7232 (mpp) cc_final: 0.6804 (mpp) REVERT: A 307 LYS cc_start: 0.7347 (mtmt) cc_final: 0.7028 (mtmt) REVERT: A 679 MET cc_start: 0.7763 (mtt) cc_final: 0.7104 (mtm) REVERT: A 809 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8100 (p0) REVERT: A 916 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7239 (mt-10) REVERT: A 921 ASP cc_start: 0.7773 (m-30) cc_final: 0.7555 (t70) REVERT: A 961 LEU cc_start: 0.6968 (tp) cc_final: 0.6713 (tp) REVERT: C 58 ASP cc_start: 0.6741 (m-30) cc_final: 0.6268 (m-30) REVERT: C 348 TRP cc_start: 0.6967 (t60) cc_final: 0.6480 (t60) REVERT: C 724 ASN cc_start: 0.6043 (m110) cc_final: 0.5806 (m-40) REVERT: C 824 ASP cc_start: 0.8983 (t0) cc_final: 0.8713 (t0) REVERT: C 938 THR cc_start: 0.7979 (p) cc_final: 0.7658 (t) REVERT: B 32 ASN cc_start: 0.7722 (m110) cc_final: 0.6902 (t0) REVERT: B 82 MET cc_start: 0.7179 (mmp) cc_final: 0.6844 (tpp) REVERT: B 209 TYR cc_start: 0.8101 (p90) cc_final: 0.7437 (p90) REVERT: B 217 TYR cc_start: 0.6251 (m-10) cc_final: 0.5922 (m-80) REVERT: B 218 PHE cc_start: 0.7679 (m-10) cc_final: 0.7459 (m-80) REVERT: B 376 MET cc_start: 0.6914 (mtt) cc_final: 0.6647 (tpt) REVERT: B 383 SER cc_start: 0.6940 (t) cc_final: 0.6548 (p) REVERT: B 470 SER cc_start: 0.7730 (m) cc_final: 0.7465 (t) REVERT: B 656 GLN cc_start: 0.7745 (mt0) cc_final: 0.7469 (mt0) REVERT: B 859 GLU cc_start: 0.8093 (pp20) cc_final: 0.7639 (tt0) REVERT: B 1005 THR cc_start: 0.7480 (m) cc_final: 0.7015 (p) REVERT: B 1108 SER cc_start: 0.8892 (t) cc_final: 0.8680 (p) REVERT: B 1197 MET cc_start: 0.8229 (mtp) cc_final: 0.7776 (mmm) outliers start: 2 outliers final: 1 residues processed: 261 average time/residue: 0.1684 time to fit residues: 74.7976 Evaluate side-chains 195 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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: 30.0000 chunk 367 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 313 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 809 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 ASN C 784 ASN C 874 ASN C1021 ASN B 169 GLN ** 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** B1103 GLN ** B1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.050145 restraints weight = 142686.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.051341 restraints weight = 87312.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052177 restraints weight = 59293.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.052684 restraints weight = 44180.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.053086 restraints weight = 35846.372| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 30080 Z= 0.251 Angle : 0.797 13.017 41089 Z= 0.405 Chirality : 0.049 0.331 4790 Planarity : 0.006 0.054 5206 Dihedral : 6.908 135.777 4060 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 0.07 % Allowed : 0.68 % Favored : 99.25 % 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: -0.93 (0.14), residues: 3491 helix: 0.49 (0.18), residues: 832 sheet: -0.26 (0.18), residues: 730 loop : -1.27 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 336 TYR 0.049 0.003 TYR C 282 PHE 0.029 0.003 PHE B 980 TRP 0.027 0.003 TRP B 192 HIS 0.014 0.002 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (29962) covalent geometry : angle 0.77614 / 0.40 (40798) SS BOND : bond 0.00519 / 0.32 ( 63) SS BOND : angle 1.51286 / 1.11 ( 126) hydrogen bonds : bond 0.05378 / 3.51 ( 1183) hydrogen bonds : angle 5.77426 / 3.98 ( 3345) link_BETA1-4 : bond 0.00609 / 0.34 ( 13) link_BETA1-4 : angle 1.81956 / 1.23 ( 39) link_NAG-ASN : bond 0.00639 / 0.41 ( 42) link_NAG-ASN : angle 2.95242 / 1.89 ( 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 237 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 235 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7243 (mtmt) cc_final: 0.7022 (mtmt) REVERT: A 433 ASP cc_start: 0.8436 (t70) cc_final: 0.8054 (t70) REVERT: A 679 MET cc_start: 0.7836 (mtt) cc_final: 0.7571 (mtm) REVERT: A 809 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8026 (p0) REVERT: A 916 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7490 (mt-10) REVERT: A 961 LEU cc_start: 0.6775 (tp) cc_final: 0.6473 (tp) REVERT: A 976 SER cc_start: 0.7703 (m) cc_final: 0.7351 (t) REVERT: A 1197 MET cc_start: 0.5780 (mmm) cc_final: 0.5544 (mmm) REVERT: C 58 ASP cc_start: 0.6889 (m-30) cc_final: 0.6295 (m-30) REVERT: C 82 MET cc_start: 0.8109 (mmm) cc_final: 0.7786 (mmm) REVERT: C 346 GLU cc_start: 0.8084 (mp0) cc_final: 0.7775 (tm-30) REVERT: B 33 ILE cc_start: 0.6005 (pt) cc_final: 0.5782 (tt) REVERT: B 82 MET cc_start: 0.7273 (mmp) cc_final: 0.6898 (tpp) REVERT: B 121 VAL cc_start: 0.7483 (t) cc_final: 0.7017 (t) REVERT: B 163 LEU cc_start: 0.8172 (tp) cc_final: 0.7909 (tp) REVERT: B 209 TYR cc_start: 0.7919 (p90) cc_final: 0.7479 (p90) REVERT: B 210 ASP cc_start: 0.6342 (t0) cc_final: 0.6094 (t0) REVERT: B 217 TYR cc_start: 0.6351 (m-10) cc_final: 0.6061 (m-80) REVERT: B 236 VAL cc_start: 0.8056 (m) cc_final: 0.7829 (m) REVERT: B 299 MET cc_start: 0.6604 (mmt) cc_final: 0.5867 (ttm) REVERT: B 376 MET cc_start: 0.6868 (mtt) cc_final: 0.6591 (tpt) REVERT: B 383 SER cc_start: 0.6576 (t) cc_final: 0.6214 (p) REVERT: B 656 GLN cc_start: 0.7665 (mt0) cc_final: 0.7286 (mt0) REVERT: B 873 MET cc_start: 0.8269 (mmp) cc_final: 0.8006 (mmt) REVERT: B 882 LEU cc_start: 0.7840 (mm) cc_final: 0.7593 (pp) REVERT: B 1182 ILE cc_start: 0.8408 (tp) cc_final: 0.8124 (tp) REVERT: B 1197 MET cc_start: 0.8269 (mtp) cc_final: 0.7851 (mmm) outliers start: 2 outliers final: 0 residues processed: 237 average time/residue: 0.1677 time to fit residues: 68.4525 Evaluate side-chains 179 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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: 2.9990 chunk 151 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 335 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 0.0030 chunk 232 optimal weight: 7.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN A1012 ASN A1028 GLN C 193 HIS C 222 GLN ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 ASN C 874 ASN B 169 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.052146 restraints weight = 139369.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.053368 restraints weight = 84508.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.054230 restraints weight = 57233.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054820 restraints weight = 42304.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055195 restraints weight = 33778.175| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30080 Z= 0.131 Angle : 0.651 11.610 41089 Z= 0.332 Chirality : 0.045 0.291 4790 Planarity : 0.004 0.055 5206 Dihedral : 6.423 138.849 4060 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 0.03 % Allowed : 0.23 % Favored : 99.74 % 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: 0.83 (0.18), residues: 850 sheet: -0.08 (0.18), residues: 749 loop : -1.09 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 280 TYR 0.031 0.002 TYR C 282 PHE 0.024 0.002 PHE C 678 TRP 0.018 0.002 TRP A 192 HIS 0.008 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (29962) covalent geometry : angle 0.63231 / 0.33 (40798) SS BOND : bond 0.00408 / 0.21 ( 63) SS BOND : angle 1.32349 / 0.99 ( 126) hydrogen bonds : bond 0.04454 / 2.89 ( 1183) hydrogen bonds : angle 5.28696 / 3.64 ( 3345) link_BETA1-4 : bond 0.00558 / 0.33 ( 13) link_BETA1-4 : angle 1.43577 / 1.03 ( 39) link_NAG-ASN : bond 0.00458 / 0.28 ( 42) link_NAG-ASN : angle 2.50234 / 1.61 ( 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 257 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.7766 (pt) cc_final: 0.7529 (pt) REVERT: A 140 TYR cc_start: 0.6429 (m-80) cc_final: 0.6179 (m-80) REVERT: A 307 LYS cc_start: 0.7326 (mtmt) cc_final: 0.6976 (mtmt) REVERT: A 433 ASP cc_start: 0.8630 (t70) cc_final: 0.8353 (t70) REVERT: A 679 MET cc_start: 0.7708 (mtt) cc_final: 0.7210 (mtm) REVERT: A 809 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.8004 (p0) REVERT: A 916 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 921 ASP cc_start: 0.7765 (m-30) cc_final: 0.7544 (t70) REVERT: A 1197 MET cc_start: 0.5765 (mmm) cc_final: 0.5453 (mmm) REVERT: C 58 ASP cc_start: 0.6645 (m-30) cc_final: 0.6156 (m-30) REVERT: C 82 MET cc_start: 0.8052 (mmm) cc_final: 0.7789 (mmm) REVERT: C 346 GLU cc_start: 0.7870 (mp0) cc_final: 0.7644 (tm-30) REVERT: C 348 TRP cc_start: 0.6812 (t60) cc_final: 0.6352 (t60) REVERT: C 661 ASP cc_start: 0.6965 (t0) cc_final: 0.6718 (t70) REVERT: C 724 ASN cc_start: 0.5951 (m110) cc_final: 0.5641 (m-40) REVERT: B 32 ASN cc_start: 0.7805 (m110) cc_final: 0.7009 (t0) REVERT: B 82 MET cc_start: 0.7195 (mmp) cc_final: 0.6820 (tpp) REVERT: B 163 LEU cc_start: 0.7939 (tp) cc_final: 0.7703 (tp) REVERT: B 209 TYR cc_start: 0.7886 (p90) cc_final: 0.7435 (p90) REVERT: B 217 TYR cc_start: 0.6109 (m-10) cc_final: 0.5839 (m-80) REVERT: B 282 TYR cc_start: 0.5532 (m-80) cc_final: 0.4882 (m-80) REVERT: B 372 MET cc_start: 0.6854 (tpp) cc_final: 0.6632 (tpp) REVERT: B 376 MET cc_start: 0.6766 (mtt) cc_final: 0.6516 (tpt) REVERT: B 383 SER cc_start: 0.6877 (t) cc_final: 0.6519 (p) REVERT: B 401 SER cc_start: 0.7916 (p) cc_final: 0.7414 (m) REVERT: B 656 GLN cc_start: 0.7710 (mt0) cc_final: 0.7414 (mt0) REVERT: B 812 GLU cc_start: 0.7308 (tp30) cc_final: 0.6476 (mt-10) REVERT: B 859 GLU cc_start: 0.8078 (pp20) cc_final: 0.7552 (tt0) REVERT: B 1197 MET cc_start: 0.8245 (mtp) cc_final: 0.7831 (mmm) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.1552 time to fit residues: 68.9677 Evaluate side-chains 188 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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: 7.9990 chunk 85 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 225 optimal weight: 0.5980 chunk 249 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN A 849 ASN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN C 874 ASN B 177 HIS ** 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** ** B1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.051506 restraints weight = 141359.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052761 restraints weight = 87532.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.053660 restraints weight = 56113.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.053795 restraints weight = 45514.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054014 restraints weight = 38884.156| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30080 Z= 0.175 Angle : 0.686 11.736 41089 Z= 0.348 Chirality : 0.046 0.288 4790 Planarity : 0.005 0.053 5206 Dihedral : 6.583 141.064 4060 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 0.03 % Allowed : 0.26 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3491 helix: 0.72 (0.18), residues: 850 sheet: -0.11 (0.19), residues: 732 loop : -1.13 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 944 TYR 0.046 0.002 TYR C 282 PHE 0.021 0.002 PHE C 678 TRP 0.018 0.002 TRP A1196 HIS 0.009 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (29962) covalent geometry : angle 0.66655 / 0.34 (40798) SS BOND : bond 0.00407 / 0.23 ( 63) SS BOND : angle 1.36758 / 1.04 ( 126) hydrogen bonds : bond 0.04649 / 3.02 ( 1183) hydrogen bonds : angle 5.40289 / 3.71 ( 3345) link_BETA1-4 : bond 0.00482 / 0.28 ( 13) link_BETA1-4 : angle 1.55399 / 1.07 ( 39) link_NAG-ASN : bond 0.00515 / 0.33 ( 42) link_NAG-ASN : angle 2.65212 / 1.68 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3992.56 seconds wall clock time: 70 minutes 27.82 seconds (4227.82 seconds total)