Starting phenix.real_space_refine on Tue Apr 16 03:15:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd9_30650/04_2024/7dd9_30650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd9_30650/04_2024/7dd9_30650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd9_30650/04_2024/7dd9_30650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd9_30650/04_2024/7dd9_30650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd9_30650/04_2024/7dd9_30650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd9_30650/04_2024/7dd9_30650.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 192 5.16 5 C 23108 2.51 5 N 6112 2.21 5 O 7725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 725": "OD1" <-> "OD2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ASP 778": "OD1" <-> "OD2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 791": "OD1" <-> "OD2" Residue "A ASP 810": "OD1" <-> "OD2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ASP 898": "OD1" <-> "OD2" Residue "A TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1048": "OE1" <-> "OE2" Residue "A GLU 1049": "OE1" <-> "OE2" Residue "A ASP 1057": "OD1" <-> "OD2" Residue "A TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1064": "OE1" <-> "OE2" Residue "A PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2081": "OD1" <-> "OD2" Residue "A ARG 2107": "NH1" <-> "NH2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C GLU 501": "OE1" <-> "OE2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C ASP 604": "OD1" <-> "OD2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 725": "OD1" <-> "OD2" Residue "C PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C ASP 778": "OD1" <-> "OD2" Residue "C TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 791": "OD1" <-> "OD2" Residue "C ASP 810": "OD1" <-> "OD2" Residue "C TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 863": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C ASP 898": "OD1" <-> "OD2" Residue "C TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1048": "OE1" <-> "OE2" Residue "C GLU 1049": "OE1" <-> "OE2" Residue "C ASP 1057": "OD1" <-> "OD2" Residue "C TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1064": "OE1" <-> "OE2" Residue "C PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2081": "OD1" <-> "OD2" Residue "C ARG 2107": "NH1" <-> "NH2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 388": "OE1" <-> "OE2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E GLU 501": "OE1" <-> "OE2" Residue "E GLU 555": "OE1" <-> "OE2" Residue "E ARG 558": "NH1" <-> "NH2" Residue "E GLU 582": "OE1" <-> "OE2" Residue "E GLU 600": "OE1" <-> "OE2" Residue "E ASP 604": "OD1" <-> "OD2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E GLU 682": "OE1" <-> "OE2" Residue "E TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 725": "OD1" <-> "OD2" Residue "E PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 768": "OE1" <-> "OE2" Residue "E ASP 778": "OD1" <-> "OD2" Residue "E TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 791": "OD1" <-> "OD2" Residue "E ASP 810": "OD1" <-> "OD2" Residue "E TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 863": "OE1" <-> "OE2" Residue "E GLU 868": "OE1" <-> "OE2" Residue "E ASP 898": "OD1" <-> "OD2" Residue "E TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1048": "OE1" <-> "OE2" Residue "E GLU 1049": "OE1" <-> "OE2" Residue "E ASP 1057": "OD1" <-> "OD2" Residue "E TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1064": "OE1" <-> "OE2" Residue "E PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2081": "OD1" <-> "OD2" Residue "E ARG 2107": "NH1" <-> "NH2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 169": "OE1" <-> "OE2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 240": "OD1" <-> "OD2" Residue "G GLU 255": "OE1" <-> "OE2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G ASP 279": "OD1" <-> "OD2" Residue "G GLU 345": "OE1" <-> "OE2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 388": "OE1" <-> "OE2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G GLU 501": "OE1" <-> "OE2" Residue "G GLU 555": "OE1" <-> "OE2" Residue "G ARG 558": "NH1" <-> "NH2" Residue "G GLU 582": "OE1" <-> "OE2" Residue "G GLU 600": "OE1" <-> "OE2" Residue "G ASP 604": "OD1" <-> "OD2" Residue "G GLU 650": "OE1" <-> "OE2" Residue "G GLU 682": "OE1" <-> "OE2" Residue "G TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 725": "OD1" <-> "OD2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 768": "OE1" <-> "OE2" Residue "G ASP 778": "OD1" <-> "OD2" Residue "G TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 791": "OD1" <-> "OD2" Residue "G ASP 810": "OD1" <-> "OD2" Residue "G TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 863": "OE1" <-> "OE2" Residue "G GLU 868": "OE1" <-> "OE2" Residue "G ASP 898": "OD1" <-> "OD2" Residue "G TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1048": "OE1" <-> "OE2" Residue "G GLU 1049": "OE1" <-> "OE2" Residue "G ASP 1057": "OD1" <-> "OD2" Residue "G TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1064": "OE1" <-> "OE2" Residue "G PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 2081": "OD1" <-> "OD2" Residue "G ARG 2107": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 37149 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 238 Classifications: {'water': 238} Link IDs: {None: 237} Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 238 Classifications: {'water': 238} Link IDs: {None: 237} Chain: "E" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 236 Classifications: {'water': 236} Link IDs: {None: 235} Chain: "G" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 237 Classifications: {'water': 237} Link IDs: {None: 236} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8784 SG CYS A2076 57.136 17.348 112.716 1.00 67.55 S ATOM 8806 SG CYS A2079 58.571 20.770 111.901 1.00 61.12 S ATOM 8964 SG CYS A2098 54.943 19.942 110.708 1.00 57.85 S ATOM 8670 SG CYS A2062 60.164 21.026 124.647 1.00 67.75 S ATOM 8691 SG CYS A2065 60.430 22.029 128.294 1.00 67.69 S ATOM 8857 SG CYS A2085 60.746 18.329 127.295 1.00 76.17 S ATOM 8882 SG CYS A2088 57.427 20.165 127.193 1.00 76.07 S ATOM 17831 SG CYS C2076 80.151 97.083 112.724 1.00 67.74 S ATOM 17853 SG CYS C2079 78.696 93.674 111.891 1.00 61.44 S ATOM 18011 SG CYS C2098 82.328 94.489 110.699 1.00 58.32 S ATOM 17717 SG CYS C2062 77.118 93.351 124.637 1.00 67.91 S ATOM 17738 SG CYS C2065 76.851 92.328 128.279 1.00 67.52 S ATOM 17904 SG CYS C2085 76.553 96.035 127.301 1.00 76.38 S ATOM 17929 SG CYS C2088 79.863 94.182 127.184 1.00 76.34 S ATOM 26878 SG CYS E2076 80.147 17.333 55.758 1.00 67.63 S ATOM 26900 SG CYS E2079 78.704 20.750 56.580 1.00 61.32 S ATOM 27058 SG CYS E2098 82.334 19.927 57.774 1.00 58.11 S ATOM 26764 SG CYS E2062 77.121 21.033 43.834 1.00 68.10 S ATOM 26785 SG CYS E2065 76.856 22.044 40.189 1.00 67.91 S ATOM 26951 SG CYS E2085 76.546 18.341 41.179 1.00 76.34 S ATOM 26976 SG CYS E2088 79.862 20.183 41.288 1.00 76.30 S ATOM 35925 SG CYS G2076 57.107 97.066 55.731 1.00 67.77 S ATOM 35947 SG CYS G2079 58.554 93.653 56.560 1.00 61.52 S ATOM 36105 SG CYS G2098 54.920 94.470 57.742 1.00 57.91 S ATOM 35811 SG CYS G2062 60.177 93.362 43.819 1.00 68.08 S ATOM 35832 SG CYS G2065 60.455 92.349 40.175 1.00 67.95 S ATOM 35998 SG CYS G2085 60.755 96.052 41.163 1.00 76.40 S ATOM 36023 SG CYS G2088 57.442 94.204 41.264 1.00 76.26 S Time building chain proxies: 18.50, per 1000 atoms: 0.50 Number of scatterers: 37149 At special positions: 0 Unit cell: (138.32, 115.44, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 12 29.99 S 192 16.00 O 7725 8.00 N 6112 7.00 C 23108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 14.30 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 615 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 290 " pdb=" ZN A1602 " pdb="ZN ZN A1602 " - pdb=" NE2 HIS A2096 " pdb="ZN ZN A1602 " - pdb=" SG CYS A2076 " pdb="ZN ZN A1602 " - pdb=" SG CYS A2079 " pdb="ZN ZN A1602 " - pdb=" SG CYS A2098 " pdb=" ZN A1603 " pdb="ZN ZN A1603 " - pdb=" SG CYS A2065 " pdb="ZN ZN A1603 " - pdb=" SG CYS A2088 " pdb="ZN ZN A1603 " - pdb=" SG CYS A2062 " pdb="ZN ZN A1603 " - pdb=" SG CYS A2085 " pdb=" ZN C1601 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 615 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 290 " pdb=" ZN C1602 " pdb="ZN ZN C1602 " - pdb=" NE2 HIS C2096 " pdb="ZN ZN C1602 " - pdb=" SG CYS C2076 " pdb="ZN ZN C1602 " - pdb=" SG CYS C2079 " pdb="ZN ZN C1602 " - pdb=" SG CYS C2098 " pdb=" ZN C1603 " pdb="ZN ZN C1603 " - pdb=" SG CYS C2065 " pdb="ZN ZN C1603 " - pdb=" SG CYS C2088 " pdb="ZN ZN C1603 " - pdb=" SG CYS C2062 " pdb="ZN ZN C1603 " - pdb=" SG CYS C2085 " pdb=" ZN E1601 " pdb="ZN ZN E1601 " - pdb=" NE2 HIS E 615 " pdb="ZN ZN E1601 " - pdb=" NE2 HIS E 290 " pdb=" ZN E1602 " pdb="ZN ZN E1602 " - pdb=" NE2 HIS E2096 " pdb="ZN ZN E1602 " - pdb=" SG CYS E2076 " pdb="ZN ZN E1602 " - pdb=" SG CYS E2079 " pdb="ZN ZN E1602 " - pdb=" SG CYS E2098 " pdb=" ZN E1603 " pdb="ZN ZN E1603 " - pdb=" SG CYS E2065 " pdb="ZN ZN E1603 " - pdb=" SG CYS E2088 " pdb="ZN ZN E1603 " - pdb=" SG CYS E2062 " pdb="ZN ZN E1603 " - pdb=" SG CYS E2085 " pdb=" ZN G1601 " pdb="ZN ZN G1601 " - pdb=" NE2 HIS G 615 " pdb="ZN ZN G1601 " - pdb=" NE2 HIS G 290 " pdb=" ZN G1602 " pdb="ZN ZN G1602 " - pdb=" NE2 HIS G2096 " pdb="ZN ZN G1602 " - pdb=" SG CYS G2076 " pdb="ZN ZN G1602 " - pdb=" SG CYS G2079 " pdb="ZN ZN G1602 " - pdb=" SG CYS G2098 " pdb=" ZN G1603 " pdb="ZN ZN G1603 " - pdb=" SG CYS G2065 " pdb="ZN ZN G1603 " - pdb=" SG CYS G2088 " pdb="ZN ZN G1603 " - pdb=" SG CYS G2062 " pdb="ZN ZN G1603 " - pdb=" SG CYS G2085 " Number of angles added : 36 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8544 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 48 sheets defined 30.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 33 through 42 removed outlier: 6.836A pdb=" N LEU A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Proline residue: A 39 - end of helix removed outlier: 3.526A pdb=" N TYR A 42 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 113 through 118 removed outlier: 4.113A pdb=" N LYS A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.805A pdb=" N TYR A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.033A pdb=" N ASN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 4.011A pdb=" N VAL A 273 " --> pdb=" O SER A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.716A pdb=" N ARG A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 465 through 475 removed outlier: 3.931A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.501A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 539 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 564 through 592 Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 623 through 653 removed outlier: 3.638A pdb=" N TYR A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) Proline residue: A 632 - end of helix Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 780 through 785 removed outlier: 3.672A pdb=" N LEU A 784 " --> pdb=" O VAL A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 882 through 888 removed outlier: 3.667A pdb=" N LYS A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 968 removed outlier: 3.685A pdb=" N VAL A 961 " --> pdb=" O ASP A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 2086 through 2091 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 24 through 27 Processing helix chain 'C' and resid 33 through 42 removed outlier: 6.836A pdb=" N LEU C 38 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Proline residue: C 39 - end of helix removed outlier: 3.526A pdb=" N TYR C 42 " --> pdb=" O PRO C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 Processing helix chain 'C' and resid 113 through 118 removed outlier: 4.113A pdb=" N LYS C 118 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 224 Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.806A pdb=" N TYR C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 4.032A pdb=" N ASN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 removed outlier: 4.012A pdb=" N VAL C 273 " --> pdb=" O SER C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.717A pdb=" N ARG C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 340 through 353 Processing helix chain 'C' and resid 372 through 391 Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 465 through 475 removed outlier: 3.932A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 3.501A pdb=" N LEU C 503 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 539 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 564 through 592 Processing helix chain 'C' and resid 598 through 612 Processing helix chain 'C' and resid 623 through 653 removed outlier: 3.638A pdb=" N TYR C 627 " --> pdb=" O ILE C 623 " (cutoff:3.500A) Proline residue: C 632 - end of helix Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 780 through 785 removed outlier: 3.672A pdb=" N LEU C 784 " --> pdb=" O VAL C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 834 Processing helix chain 'C' and resid 882 through 888 removed outlier: 3.667A pdb=" N LYS C 888 " --> pdb=" O TRP C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 968 removed outlier: 3.685A pdb=" N VAL C 961 " --> pdb=" O ASP C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 2086 through 2091 Processing helix chain 'E' and resid 16 through 23 Processing helix chain 'E' and resid 24 through 27 Processing helix chain 'E' and resid 33 through 42 removed outlier: 6.836A pdb=" N LEU E 38 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Proline residue: E 39 - end of helix removed outlier: 3.526A pdb=" N TYR E 42 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 Processing helix chain 'E' and resid 113 through 118 removed outlier: 4.113A pdb=" N LYS E 118 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 224 Processing helix chain 'E' and resid 228 through 245 removed outlier: 3.806A pdb=" N TYR E 232 " --> pdb=" O CYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.032A pdb=" N ASN E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 removed outlier: 4.011A pdb=" N VAL E 273 " --> pdb=" O SER E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 320 removed outlier: 3.717A pdb=" N ARG E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 307 " --> pdb=" O ARG E 303 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR E 312 " --> pdb=" O ARG E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 340 Processing helix chain 'E' and resid 340 through 353 Processing helix chain 'E' and resid 372 through 391 Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'E' and resid 425 through 430 Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.931A pdb=" N ILE E 473 " --> pdb=" O VAL E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 516 removed outlier: 3.501A pdb=" N LEU E 503 " --> pdb=" O THR E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 539 Processing helix chain 'E' and resid 557 through 562 Processing helix chain 'E' and resid 564 through 592 Processing helix chain 'E' and resid 598 through 612 Processing helix chain 'E' and resid 623 through 653 removed outlier: 3.638A pdb=" N TYR E 627 " --> pdb=" O ILE E 623 " (cutoff:3.500A) Proline residue: E 632 - end of helix Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 780 through 785 removed outlier: 3.672A pdb=" N LEU E 784 " --> pdb=" O VAL E 781 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 834 Processing helix chain 'E' and resid 882 through 888 removed outlier: 3.669A pdb=" N LYS E 888 " --> pdb=" O TRP E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 957 through 968 removed outlier: 3.685A pdb=" N VAL E 961 " --> pdb=" O ASP E 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 2086 through 2091 Processing helix chain 'G' and resid 16 through 23 Processing helix chain 'G' and resid 24 through 27 Processing helix chain 'G' and resid 33 through 42 removed outlier: 6.835A pdb=" N LEU G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Proline residue: G 39 - end of helix removed outlier: 3.526A pdb=" N TYR G 42 " --> pdb=" O PRO G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 113 through 118 removed outlier: 4.114A pdb=" N LYS G 118 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 224 Processing helix chain 'G' and resid 228 through 245 removed outlier: 3.804A pdb=" N TYR G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 265 removed outlier: 4.032A pdb=" N ASN G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA G 262 " --> pdb=" O ASN G 258 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE G 263 " --> pdb=" O LEU G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 276 removed outlier: 4.011A pdb=" N VAL G 273 " --> pdb=" O SER G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 320 removed outlier: 3.717A pdb=" N ARG G 304 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 307 " --> pdb=" O ARG G 303 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR G 312 " --> pdb=" O ARG G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 340 Processing helix chain 'G' and resid 340 through 353 Processing helix chain 'G' and resid 372 through 391 Processing helix chain 'G' and resid 409 through 417 Processing helix chain 'G' and resid 425 through 430 Processing helix chain 'G' and resid 465 through 475 removed outlier: 3.931A pdb=" N ILE G 473 " --> pdb=" O VAL G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 516 Processing helix chain 'G' and resid 527 through 539 Processing helix chain 'G' and resid 557 through 562 Processing helix chain 'G' and resid 564 through 592 Processing helix chain 'G' and resid 598 through 612 Processing helix chain 'G' and resid 623 through 653 removed outlier: 3.638A pdb=" N TYR G 627 " --> pdb=" O ILE G 623 " (cutoff:3.500A) Proline residue: G 632 - end of helix Processing helix chain 'G' and resid 662 through 664 No H-bonds generated for 'chain 'G' and resid 662 through 664' Processing helix chain 'G' and resid 780 through 785 removed outlier: 3.671A pdb=" N LEU G 784 " --> pdb=" O VAL G 781 " (cutoff:3.500A) Processing helix chain 'G' and resid 830 through 834 Processing helix chain 'G' and resid 882 through 888 removed outlier: 3.668A pdb=" N LYS G 888 " --> pdb=" O TRP G 884 " (cutoff:3.500A) Processing helix chain 'G' and resid 957 through 968 removed outlier: 3.685A pdb=" N VAL G 961 " --> pdb=" O ASP G 957 " (cutoff:3.500A) Processing helix chain 'G' and resid 2086 through 2091 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.991A pdb=" N GLU A 89 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 65 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN A 143 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.622A pdb=" N PHE A 193 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.264A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 284 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A 489 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 286 " --> pdb=" O PHE A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.264A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.685A pdb=" N ARG A 972 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 666 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AA8, first strand: chain 'A' and resid 787 through 790 removed outlier: 4.680A pdb=" N TYR A 764 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS A 850 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A 929 " --> pdb=" O LYS A 850 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 852 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 922 " --> pdb=" O HIS A 919 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY A 915 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 800 removed outlier: 6.505A pdb=" N SER A 806 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER A 800 " --> pdb=" O ARG A 804 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE A 896 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER A 900 " --> pdb=" O PHE A 864 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE A 864 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 989 through 993 Processing sheet with id=AB2, first strand: chain 'A' and resid 997 through 1004 removed outlier: 5.521A pdb=" N LEU A 999 " --> pdb=" O TYR A1016 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A1016 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A1072 " --> pdb=" O CYS A1040 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A1037 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU A1049 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS A1039 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2083 through 2085 Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.991A pdb=" N GLU C 89 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 65 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 143 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.621A pdb=" N PHE C 193 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE C 284 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE C 489 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE C 286 " --> pdb=" O PHE C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AB9, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.685A pdb=" N ARG C 972 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 666 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AC2, first strand: chain 'C' and resid 787 through 790 removed outlier: 4.680A pdb=" N TYR C 764 " --> pdb=" O LEU C 790 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS C 850 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG C 929 " --> pdb=" O LYS C 850 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 852 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 922 " --> pdb=" O HIS C 919 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY C 915 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 794 through 800 removed outlier: 6.505A pdb=" N SER C 806 " --> pdb=" O LYS C 798 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 800 " --> pdb=" O ARG C 804 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG C 804 " --> pdb=" O SER C 800 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER C 817 " --> pdb=" O ILE C 813 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE C 896 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER C 900 " --> pdb=" O PHE C 864 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE C 864 " --> pdb=" O SER C 900 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 989 through 993 Processing sheet with id=AC5, first strand: chain 'C' and resid 997 through 1004 removed outlier: 5.465A pdb=" N LEU C 999 " --> pdb=" O TYR C1016 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR C1016 " --> pdb=" O LEU C 999 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C1072 " --> pdb=" O CYS C1040 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL C1037 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU C1049 " --> pdb=" O VAL C1037 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS C1039 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 2083 through 2085 Processing sheet with id=AC7, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.992A pdb=" N GLU E 89 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU E 65 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN E 143 " --> pdb=" O VAL E 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.621A pdb=" N PHE E 193 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE E 325 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL E 326 " --> pdb=" O ALA E 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY E 287 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE E 284 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE E 489 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE E 286 " --> pdb=" O PHE E 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE E 325 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL E 326 " --> pdb=" O ALA E 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY E 287 " --> pdb=" O VAL E 326 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 397 through 399 Processing sheet with id=AD3, first strand: chain 'E' and resid 654 through 656 removed outlier: 3.685A pdb=" N ARG E 972 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU E 666 " --> pdb=" O ALA E 702 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'E' and resid 787 through 790 removed outlier: 4.679A pdb=" N TYR E 764 " --> pdb=" O LEU E 790 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS E 850 " --> pdb=" O ARG E 929 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG E 929 " --> pdb=" O LYS E 850 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU E 852 " --> pdb=" O LEU E 927 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 922 " --> pdb=" O HIS E 919 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY E 915 " --> pdb=" O SER E 926 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 794 through 800 removed outlier: 6.505A pdb=" N SER E 806 " --> pdb=" O LYS E 798 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER E 800 " --> pdb=" O ARG E 804 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG E 804 " --> pdb=" O SER E 800 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER E 817 " --> pdb=" O ILE E 813 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE E 896 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER E 900 " --> pdb=" O PHE E 864 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE E 864 " --> pdb=" O SER E 900 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 989 through 993 Processing sheet with id=AD8, first strand: chain 'E' and resid 997 through 1004 removed outlier: 5.465A pdb=" N LEU E 999 " --> pdb=" O TYR E1016 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR E1016 " --> pdb=" O LEU E 999 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR E1072 " --> pdb=" O CYS E1040 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL E1037 " --> pdb=" O GLU E1049 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU E1049 " --> pdb=" O VAL E1037 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS E1039 " --> pdb=" O LEU E1047 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 2083 through 2085 Processing sheet with id=AE1, first strand: chain 'G' and resid 89 through 91 removed outlier: 3.991A pdb=" N GLU G 89 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU G 65 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN G 143 " --> pdb=" O VAL G 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 96 through 97 removed outlier: 3.621A pdb=" N PHE G 193 " --> pdb=" O PHE G 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE G 325 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL G 326 " --> pdb=" O ALA G 285 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY G 287 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE G 284 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE G 489 " --> pdb=" O PHE G 284 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE G 286 " --> pdb=" O PHE G 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE G 325 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL G 326 " --> pdb=" O ALA G 285 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY G 287 " --> pdb=" O VAL G 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 397 through 399 Processing sheet with id=AE6, first strand: chain 'G' and resid 654 through 656 removed outlier: 3.685A pdb=" N ARG G 972 " --> pdb=" O LEU G 669 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU G 666 " --> pdb=" O ALA G 702 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 712 through 715 Processing sheet with id=AE8, first strand: chain 'G' and resid 787 through 790 removed outlier: 4.681A pdb=" N TYR G 764 " --> pdb=" O LEU G 790 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS G 850 " --> pdb=" O ARG G 929 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG G 929 " --> pdb=" O LYS G 850 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU G 852 " --> pdb=" O LEU G 927 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 922 " --> pdb=" O HIS G 919 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY G 915 " --> pdb=" O SER G 926 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 794 through 800 removed outlier: 6.504A pdb=" N SER G 806 " --> pdb=" O LYS G 798 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER G 800 " --> pdb=" O ARG G 804 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG G 804 " --> pdb=" O SER G 800 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER G 817 " --> pdb=" O ILE G 813 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE G 896 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER G 900 " --> pdb=" O PHE G 864 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE G 864 " --> pdb=" O SER G 900 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 989 through 993 Processing sheet with id=AF2, first strand: chain 'G' and resid 997 through 1004 removed outlier: 5.465A pdb=" N LEU G 999 " --> pdb=" O TYR G1016 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR G1016 " --> pdb=" O LEU G 999 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR G1072 " --> pdb=" O CYS G1040 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL G1037 " --> pdb=" O GLU G1049 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU G1049 " --> pdb=" O VAL G1037 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS G1039 " --> pdb=" O LEU G1047 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 2083 through 2085 1549 hydrogen bonds defined for protein. 4203 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: 19.97 Time building geometry restraints manager: 15.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11737 1.34 - 1.46: 7677 1.46 - 1.58: 17450 1.58 - 1.70: 0 1.70 - 1.81: 260 Bond restraints: 37124 Sorted by residual: bond pdb=" CB MET A 242 " pdb=" CG MET A 242 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.58e+00 bond pdb=" CB MET E 242 " pdb=" CG MET E 242 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.58e+00 bond pdb=" CB MET G 242 " pdb=" CG MET G 242 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.46e+00 bond pdb=" CB MET C 242 " pdb=" CG MET C 242 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.46e+00 bond pdb=" SD MET G 242 " pdb=" CE MET G 242 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.88e+00 ... (remaining 37119 not shown) Histogram of bond angle deviations from ideal: 95.95 - 103.58: 444 103.58 - 111.20: 14793 111.20 - 118.82: 14703 118.82 - 126.44: 19755 126.44 - 134.07: 677 Bond angle restraints: 50372 Sorted by residual: angle pdb=" N GLU E1017 " pdb=" CA GLU E1017 " pdb=" C GLU E1017 " ideal model delta sigma weight residual 109.76 101.24 8.52 1.59e+00 3.96e-01 2.87e+01 angle pdb=" N GLU C1017 " pdb=" CA GLU C1017 " pdb=" C GLU C1017 " ideal model delta sigma weight residual 109.76 101.27 8.49 1.59e+00 3.96e-01 2.85e+01 angle pdb=" N GLU G1017 " pdb=" CA GLU G1017 " pdb=" C GLU G1017 " ideal model delta sigma weight residual 109.76 101.29 8.47 1.59e+00 3.96e-01 2.84e+01 angle pdb=" N ASP A 742 " pdb=" CA ASP A 742 " pdb=" C ASP A 742 " ideal model delta sigma weight residual 109.76 102.73 7.03 1.59e+00 3.96e-01 1.95e+01 angle pdb=" N ASP E 742 " pdb=" CA ASP E 742 " pdb=" C ASP E 742 " ideal model delta sigma weight residual 109.76 102.74 7.02 1.59e+00 3.96e-01 1.95e+01 ... (remaining 50367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 19341 17.85 - 35.69: 2084 35.69 - 53.54: 483 53.54 - 71.38: 76 71.38 - 89.23: 44 Dihedral angle restraints: 22028 sinusoidal: 8820 harmonic: 13208 Sorted by residual: dihedral pdb=" CA TYR A 42 " pdb=" C TYR A 42 " pdb=" N ASP A 43 " pdb=" CA ASP A 43 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA TYR G 42 " pdb=" C TYR G 42 " pdb=" N ASP G 43 " pdb=" CA ASP G 43 " ideal model delta harmonic sigma weight residual 180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA TYR C 42 " pdb=" C TYR C 42 " pdb=" N ASP C 43 " pdb=" CA ASP C 43 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 22025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3624 0.047 - 0.094: 1407 0.094 - 0.141: 398 0.141 - 0.189: 27 0.189 - 0.236: 8 Chirality restraints: 5464 Sorted by residual: chirality pdb=" CA GLU E1017 " pdb=" N GLU E1017 " pdb=" C GLU E1017 " pdb=" CB GLU E1017 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLU G1017 " pdb=" N GLU G1017 " pdb=" C GLU G1017 " pdb=" CB GLU G1017 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA GLU C1017 " pdb=" N GLU C1017 " pdb=" C GLU C1017 " pdb=" CB GLU C1017 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 5461 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 159 " -0.022 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP A 159 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 159 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 159 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 159 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 159 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 159 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 159 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 159 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 159 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 159 " 0.022 2.00e-02 2.50e+03 1.14e-02 3.22e+00 pdb=" CG TRP E 159 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP E 159 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP E 159 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 159 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 159 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 159 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 159 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 159 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 159 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 159 " -0.022 2.00e-02 2.50e+03 1.12e-02 3.16e+00 pdb=" CG TRP G 159 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 159 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP G 159 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP G 159 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 159 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 159 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 159 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 159 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 159 " -0.003 2.00e-02 2.50e+03 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 417 2.53 - 3.12: 28351 3.12 - 3.71: 63155 3.71 - 4.31: 100637 4.31 - 4.90: 155639 Nonbonded interactions: 348199 Sorted by model distance: nonbonded pdb=" OD2 ASP C 402 " pdb="ZN ZN C1601 " model vdw 1.932 2.230 nonbonded pdb=" OD2 ASP G 402 " pdb="ZN ZN G1601 " model vdw 1.933 2.230 nonbonded pdb=" OD2 ASP A 402 " pdb="ZN ZN A1601 " model vdw 1.933 2.230 nonbonded pdb=" OD2 ASP E 402 " pdb="ZN ZN E1601 " model vdw 1.933 2.230 nonbonded pdb=" OD1 ASP E 292 " pdb="ZN ZN E1601 " model vdw 1.986 2.230 ... (remaining 348194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.050 Extract box with map and model: 8.460 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 107.070 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.007 0.077 37124 Z= 0.481 Angle : 0.711 10.089 50372 Z= 0.391 Chirality : 0.052 0.236 5464 Planarity : 0.004 0.044 6516 Dihedral : 15.884 89.231 13484 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.93 % Allowed : 16.57 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.12), residues: 4500 helix: 0.77 (0.15), residues: 1156 sheet: -0.39 (0.14), residues: 1136 loop : -1.90 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 159 HIS 0.005 0.001 HIS C 476 PHE 0.019 0.002 PHE C 325 TYR 0.021 0.002 TYR G 627 ARG 0.006 0.000 ARG E1026 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 322 time to evaluate : 4.544 Fit side-chains REVERT: A 48 ASP cc_start: 0.7674 (p0) cc_final: 0.7412 (p0) REVERT: C 48 ASP cc_start: 0.7685 (p0) cc_final: 0.7414 (p0) REVERT: E 48 ASP cc_start: 0.7684 (p0) cc_final: 0.7408 (p0) REVERT: G 48 ASP cc_start: 0.7683 (p0) cc_final: 0.7408 (p0) outliers start: 77 outliers final: 51 residues processed: 396 average time/residue: 1.6889 time to fit residues: 802.1348 Evaluate side-chains 342 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 291 time to evaluate : 4.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 2084 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 543 GLN Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 2084 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 824 SER Chi-restraints excluded: chain E residue 953 SER Chi-restraints excluded: chain E residue 987 ASP Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 596 SER Chi-restraints excluded: chain G residue 824 SER Chi-restraints excluded: chain G residue 953 SER Chi-restraints excluded: chain G residue 987 ASP Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1057 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 378 optimal weight: 4.9990 chunk 339 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 213 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 406 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 248 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS A 775 GLN A 894 GLN A 921 ASN C 236 GLN C 248 ASN ** C 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 HIS C 775 GLN C 894 GLN C 921 ASN E 236 GLN E 248 ASN ** E 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 744 HIS E 775 GLN E 894 GLN E 921 ASN G 236 GLN G 248 ASN ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 744 HIS G 775 GLN G 894 GLN G 921 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37124 Z= 0.190 Angle : 0.571 7.036 50372 Z= 0.308 Chirality : 0.045 0.162 5464 Planarity : 0.004 0.034 6516 Dihedral : 6.930 57.904 4923 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.97 % Allowed : 16.40 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.12), residues: 4500 helix: 1.21 (0.15), residues: 1144 sheet: -0.52 (0.14), residues: 1140 loop : -1.74 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 159 HIS 0.004 0.001 HIS C 453 PHE 0.016 0.001 PHE G 896 TYR 0.015 0.001 TYR G 627 ARG 0.003 0.000 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 335 time to evaluate : 4.324 Fit side-chains REVERT: A 46 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7397 (ttm-80) REVERT: A 48 ASP cc_start: 0.7646 (p0) cc_final: 0.7413 (p0) REVERT: A 423 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8998 (tm) REVERT: C 46 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7391 (ttm-80) REVERT: C 48 ASP cc_start: 0.7653 (p0) cc_final: 0.7406 (p0) REVERT: C 423 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8996 (tm) REVERT: E 46 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7378 (ttm-80) REVERT: E 48 ASP cc_start: 0.7653 (p0) cc_final: 0.7407 (p0) REVERT: E 423 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8997 (tm) REVERT: G 46 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7389 (ttm-80) REVERT: G 48 ASP cc_start: 0.7649 (p0) cc_final: 0.7403 (p0) REVERT: G 423 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8996 (tm) outliers start: 119 outliers final: 28 residues processed: 425 average time/residue: 1.6397 time to fit residues: 840.0447 Evaluate side-chains 335 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 299 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1057 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 338 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 chunk 440 optimal weight: 3.9990 chunk 362 optimal weight: 0.0570 chunk 404 optimal weight: 6.9990 chunk 138 optimal weight: 0.0170 chunk 326 optimal weight: 8.9990 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 248 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN C 236 GLN C 248 ASN ** C 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 921 ASN E 236 GLN E 248 ASN ** E 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 GLN E 921 ASN G 236 GLN G 248 ASN ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 37124 Z= 0.384 Angle : 0.658 8.340 50372 Z= 0.354 Chirality : 0.050 0.183 5464 Planarity : 0.005 0.056 6516 Dihedral : 6.618 39.713 4876 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.70 % Allowed : 16.88 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 4500 helix: 1.14 (0.15), residues: 1136 sheet: -0.55 (0.14), residues: 1140 loop : -1.77 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 159 HIS 0.006 0.001 HIS G 476 PHE 0.019 0.002 PHE A 325 TYR 0.017 0.002 TYR A 627 ARG 0.004 0.000 ARG C 929 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 328 time to evaluate : 3.980 Fit side-chains REVERT: A 46 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7354 (ttm-80) REVERT: A 48 ASP cc_start: 0.7691 (p0) cc_final: 0.7450 (p0) REVERT: A 175 MET cc_start: 0.7892 (mmm) cc_final: 0.7412 (mmm) REVERT: A 692 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7495 (pp20) REVERT: C 48 ASP cc_start: 0.7756 (p0) cc_final: 0.7486 (p0) REVERT: C 175 MET cc_start: 0.7933 (mmm) cc_final: 0.7446 (mmm) REVERT: E 46 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7383 (ttm-80) REVERT: E 48 ASP cc_start: 0.7697 (p0) cc_final: 0.7453 (p0) REVERT: E 175 MET cc_start: 0.7929 (mmm) cc_final: 0.7443 (mmm) REVERT: G 46 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7344 (ttm-80) REVERT: G 48 ASP cc_start: 0.7696 (p0) cc_final: 0.7450 (p0) REVERT: G 175 MET cc_start: 0.7926 (mmm) cc_final: 0.7438 (mmm) outliers start: 108 outliers final: 35 residues processed: 417 average time/residue: 1.6966 time to fit residues: 847.1682 Evaluate side-chains 354 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 315 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 543 GLN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 734 ASN Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 734 ASN Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 402 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 194 optimal weight: 5.9990 chunk 273 optimal weight: 0.7980 chunk 409 optimal weight: 0.9990 chunk 433 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 387 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 775 GLN A 921 ASN C 248 ASN ** C 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 921 ASN E 248 ASN ** E 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 GLN E 921 ASN G 248 ASN ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37124 Z= 0.180 Angle : 0.562 13.572 50372 Z= 0.297 Chirality : 0.044 0.158 5464 Planarity : 0.003 0.034 6516 Dihedral : 6.048 39.540 4868 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.02 % Allowed : 16.98 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4500 helix: 1.38 (0.16), residues: 1144 sheet: -0.63 (0.14), residues: 1124 loop : -1.69 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 777 HIS 0.003 0.001 HIS C 453 PHE 0.016 0.001 PHE A 896 TYR 0.012 0.001 TYR A 627 ARG 0.002 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 341 time to evaluate : 4.828 Fit side-chains REVERT: A 46 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7350 (ttm-80) REVERT: A 48 ASP cc_start: 0.7785 (p0) cc_final: 0.7510 (p0) REVERT: A 111 ARG cc_start: 0.7740 (ttt-90) cc_final: 0.7352 (ttm170) REVERT: A 175 MET cc_start: 0.7670 (mmm) cc_final: 0.7303 (mmm) REVERT: A 378 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8517 (mmt90) REVERT: C 46 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7044 (ttm-80) REVERT: C 48 ASP cc_start: 0.7706 (p0) cc_final: 0.7440 (p0) REVERT: C 111 ARG cc_start: 0.7733 (ttt-90) cc_final: 0.7336 (ttm170) REVERT: C 175 MET cc_start: 0.7673 (mmm) cc_final: 0.7322 (mmm) REVERT: E 46 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7337 (ttm-80) REVERT: E 48 ASP cc_start: 0.7785 (p0) cc_final: 0.7504 (p0) REVERT: E 175 MET cc_start: 0.7672 (mmm) cc_final: 0.7319 (mmm) REVERT: G 46 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7337 (ttm-80) REVERT: G 48 ASP cc_start: 0.7783 (p0) cc_final: 0.7500 (p0) REVERT: G 111 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.7351 (ttm170) REVERT: G 175 MET cc_start: 0.7672 (mmm) cc_final: 0.7316 (mmm) outliers start: 121 outliers final: 35 residues processed: 439 average time/residue: 1.5053 time to fit residues: 789.4054 Evaluate side-chains 342 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 302 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 543 GLN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 1057 ASP Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 360 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 322 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 369 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN C 248 ASN ** C 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 921 ASN E 248 ASN ** E 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 GLN E 921 ASN G 248 ASN ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 37124 Z= 0.495 Angle : 0.720 13.567 50372 Z= 0.383 Chirality : 0.053 0.209 5464 Planarity : 0.005 0.068 6516 Dihedral : 6.538 42.338 4856 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.65 % Allowed : 17.82 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 4500 helix: 0.97 (0.15), residues: 1160 sheet: -0.57 (0.14), residues: 1136 loop : -1.83 (0.12), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP G 159 HIS 0.008 0.002 HIS A 476 PHE 0.020 0.003 PHE G 325 TYR 0.018 0.003 TYR E 406 ARG 0.005 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 323 time to evaluate : 4.346 Fit side-chains REVERT: A 46 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7486 (ttm-80) REVERT: A 48 ASP cc_start: 0.7745 (p0) cc_final: 0.7457 (p0) REVERT: A 131 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: C 46 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7384 (ttm-80) REVERT: C 48 ASP cc_start: 0.7761 (p0) cc_final: 0.7481 (p0) REVERT: C 131 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: E 46 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7494 (ttm-80) REVERT: E 48 ASP cc_start: 0.7744 (p0) cc_final: 0.7454 (p0) REVERT: E 131 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: G 46 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7492 (ttm-80) REVERT: G 48 ASP cc_start: 0.7744 (p0) cc_final: 0.7450 (p0) REVERT: G 131 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7661 (mm-30) outliers start: 106 outliers final: 48 residues processed: 403 average time/residue: 1.8043 time to fit residues: 860.8535 Evaluate side-chains 378 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 322 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 543 GLN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 734 ASN Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 734 ASN Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1057 ASP Chi-restraints excluded: chain G residue 1060 GLU Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 145 optimal weight: 1.9990 chunk 389 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 433 optimal weight: 0.7980 chunk 359 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 227 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 475 GLN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN A1076 ASN C 248 ASN C 475 GLN C 775 GLN C 921 ASN C1076 ASN E 248 ASN E 475 GLN E 775 GLN E 921 ASN E1076 ASN G 248 ASN G 475 GLN G 775 GLN G 921 ASN G1076 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37124 Z= 0.169 Angle : 0.564 12.584 50372 Z= 0.298 Chirality : 0.044 0.157 5464 Planarity : 0.003 0.036 6516 Dihedral : 5.963 40.477 4856 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.20 % Allowed : 18.23 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4500 helix: 1.37 (0.16), residues: 1136 sheet: -0.71 (0.14), residues: 1132 loop : -1.66 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 777 HIS 0.003 0.001 HIS A 453 PHE 0.016 0.001 PHE A 896 TYR 0.013 0.001 TYR A 627 ARG 0.002 0.000 ARG E 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 342 time to evaluate : 4.283 Fit side-chains REVERT: A 46 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7356 (ttm-80) REVERT: A 48 ASP cc_start: 0.7745 (p0) cc_final: 0.7490 (p0) REVERT: A 131 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: C 46 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7049 (ttm-80) REVERT: C 48 ASP cc_start: 0.7741 (p0) cc_final: 0.7480 (p0) REVERT: C 131 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: E 46 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7349 (ttm-80) REVERT: E 48 ASP cc_start: 0.7747 (p0) cc_final: 0.7490 (p0) REVERT: E 175 MET cc_start: 0.7644 (mmm) cc_final: 0.7222 (mmm) REVERT: G 46 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7347 (ttm-80) REVERT: G 48 ASP cc_start: 0.7743 (p0) cc_final: 0.7484 (p0) REVERT: G 131 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7562 (mm-30) outliers start: 88 outliers final: 39 residues processed: 412 average time/residue: 1.7732 time to fit residues: 867.1775 Evaluate side-chains 372 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 326 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 543 GLN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 810 ASP Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 810 ASP Chi-restraints excluded: chain G residue 1057 ASP Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 417 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 364 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 431 optimal weight: 0.5980 chunk 270 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 475 GLN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN C 248 ASN C 475 GLN C 775 GLN C 921 ASN E 248 ASN E 475 GLN E 775 GLN E 921 ASN G 248 ASN G 475 GLN G 775 GLN G 921 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37124 Z= 0.220 Angle : 0.583 11.764 50372 Z= 0.307 Chirality : 0.045 0.163 5464 Planarity : 0.004 0.035 6516 Dihedral : 5.959 40.752 4856 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.50 % Allowed : 18.10 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.12), residues: 4500 helix: 1.44 (0.16), residues: 1140 sheet: -0.68 (0.14), residues: 1124 loop : -1.66 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 777 HIS 0.004 0.001 HIS A 453 PHE 0.016 0.002 PHE C 896 TYR 0.014 0.002 TYR G 627 ARG 0.003 0.000 ARG G 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 320 time to evaluate : 4.321 Fit side-chains REVERT: A 46 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7394 (ttm-80) REVERT: A 48 ASP cc_start: 0.7765 (p0) cc_final: 0.7469 (p0) REVERT: A 175 MET cc_start: 0.7748 (mmm) cc_final: 0.7384 (mmm) REVERT: C 46 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7155 (ttm-80) REVERT: C 48 ASP cc_start: 0.7787 (p0) cc_final: 0.7527 (p0) REVERT: C 131 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: E 46 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7382 (ttm-80) REVERT: E 48 ASP cc_start: 0.7767 (p0) cc_final: 0.7507 (p0) REVERT: E 175 MET cc_start: 0.7686 (mmm) cc_final: 0.7276 (mmm) REVERT: G 46 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7381 (ttm-80) REVERT: G 48 ASP cc_start: 0.7765 (p0) cc_final: 0.7502 (p0) REVERT: G 175 MET cc_start: 0.7742 (mmm) cc_final: 0.7380 (mmm) outliers start: 100 outliers final: 52 residues processed: 399 average time/residue: 1.7012 time to fit residues: 803.2432 Evaluate side-chains 369 residues out of total 4004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 312 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 543 GLN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 810 ASP Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 596 SER Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 810 ASP Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1057 ASP Chi-restraints excluded: chain G residue 1060 GLU Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 267 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 339 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: