Starting phenix.real_space_refine on Mon Feb 19 19:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6r_26378/02_2024/7u6r_26378.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6r_26378/02_2024/7u6r_26378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6r_26378/02_2024/7u6r_26378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6r_26378/02_2024/7u6r_26378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6r_26378/02_2024/7u6r_26378.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6r_26378/02_2024/7u6r_26378.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.191 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 16434 2.51 5 N 4215 2.21 5 O 4774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 66": "NH1" <-> "NH2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 884": "OE1" <-> "OE2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A ASP 903": "OD1" <-> "OD2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1051": "OD1" <-> "OD2" Residue "A GLU 1140": "OE1" <-> "OE2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1171": "NH1" <-> "NH2" Residue "A ASP 1175": "OD1" <-> "OD2" Residue "A ARG 1195": "NH1" <-> "NH2" Residue "A TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 426": "OE1" <-> "OE2" Residue "B PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 884": "OE1" <-> "OE2" Residue "B PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B ASP 903": "OD1" <-> "OD2" Residue "B TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1051": "OD1" <-> "OD2" Residue "B GLU 1140": "OE1" <-> "OE2" Residue "B TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1171": "NH1" <-> "NH2" Residue "B ASP 1175": "OD1" <-> "OD2" Residue "B ARG 1195": "NH1" <-> "NH2" Residue "B TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "C TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 884": "OE1" <-> "OE2" Residue "C PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 902": "OD1" <-> "OD2" Residue "C ASP 903": "OD1" <-> "OD2" Residue "C TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1051": "OD1" <-> "OD2" Residue "C GLU 1140": "OE1" <-> "OE2" Residue "C TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C ASP 1175": "OD1" <-> "OD2" Residue "C ARG 1195": "NH1" <-> "NH2" Residue "C TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25561 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8282 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 51, 'TRANS': 1045} Chain breaks: 11 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 10, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 146 Chain: "B" Number of atoms: 8283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8283 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 51, 'TRANS': 1045} Chain breaks: 11 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 10, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 146 Chain: "C" Number of atoms: 8282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8282 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 51, 'TRANS': 1045} Chain breaks: 11 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 10, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 146 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 13.91, per 1000 atoms: 0.54 Number of scatterers: 25561 At special positions: 0 Unit cell: (131.25, 132.3, 155.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 4774 8.00 N 4215 7.00 C 16434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 199 " distance=2.02 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.02 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 411 " distance=2.02 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 482 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 583 " distance=2.29 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 651 " distance=2.02 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS A 711 " distance=2.05 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 734 " distance=2.02 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 820 " distance=2.14 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 809 " distance=2.16 Simple disulfide: pdb=" SG CYS A 904 " - pdb=" SG CYS A 917 " distance=2.10 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.02 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 199 " distance=2.02 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 411 " distance=2.02 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 583 " distance=2.29 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 651 " distance=2.02 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 711 " distance=2.05 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 734 " distance=2.02 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 820 " distance=2.14 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 809 " distance=2.16 Simple disulfide: pdb=" SG CYS B 904 " - pdb=" SG CYS B 917 " distance=2.10 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1109 " distance=2.02 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 199 " distance=2.02 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 353 " distance=2.02 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 411 " distance=2.02 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 583 " distance=2.29 Simple disulfide: pdb=" SG CYS C 506 " - pdb=" SG CYS C 527 " distance=2.03 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 651 " distance=2.02 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 676 " - pdb=" SG CYS C 711 " distance=2.05 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 734 " distance=2.02 Simple disulfide: pdb=" SG CYS C 798 " - pdb=" SG CYS C 820 " distance=2.14 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 809 " distance=2.16 Simple disulfide: pdb=" SG CYS C 904 " - pdb=" SG CYS C 917 " distance=2.10 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.02 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1156 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1401 " - " ASN A 70 " " NAG A1402 " - " ASN A 108 " " NAG A1403 " - " ASN A 158 " " NAG A1404 " - " ASN A 862 " " NAG A1405 " - " ASN A 388 " " NAG A1406 " - " ASN A 594 " " NAG A1407 " - " ASN A1167 " " NAG A1408 " - " ASN A 240 " " NAG A1409 " - " ASN A 248 " " NAG A1410 " - " ASN A 777 " " NAG A1411 " - " ASN A1205 " " NAG A1412 " - " ASN A 719 " " NAG A1413 " - " ASN A 489 " " NAG B1401 " - " ASN B 70 " " NAG B1402 " - " ASN B 108 " " NAG B1403 " - " ASN B 158 " " NAG B1404 " - " ASN B 862 " " NAG B1405 " - " ASN B 388 " " NAG B1406 " - " ASN B 594 " " NAG B1407 " - " ASN B1167 " " NAG B1408 " - " ASN B 240 " " NAG B1409 " - " ASN B 248 " " NAG B1410 " - " ASN B 777 " " NAG B1411 " - " ASN B1205 " " NAG B1412 " - " ASN B 719 " " NAG B1413 " - " ASN B 489 " " NAG C1401 " - " ASN C 70 " " NAG C1402 " - " ASN C 108 " " NAG C1403 " - " ASN C 158 " " NAG C1404 " - " ASN C 862 " " NAG C1405 " - " ASN C 388 " " NAG C1406 " - " ASN C 594 " " NAG C1407 " - " ASN C1167 " " NAG C1408 " - " ASN C 240 " " NAG C1409 " - " ASN C 248 " " NAG C1410 " - " ASN C 777 " " NAG C1411 " - " ASN C1205 " " NAG C1412 " - " ASN C 719 " " NAG C1413 " - " ASN C 489 " " NAG D 1 " - " ASN A 414 " " NAG E 1 " - " ASN A 170 " " NAG F 1 " - " ASN B 414 " " NAG G 1 " - " ASN B 170 " " NAG H 1 " - " ASN C 414 " " NAG I 1 " - " ASN C 170 " Time building additional restraints: 10.95 Conformation dependent library (CDL) restraints added in 4.9 seconds 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6126 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 48 sheets defined 28.7% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 346 through 356 Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.956A pdb=" N PHE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.690A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.608A pdb=" N ASN A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 561 Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 676 through 682 removed outlier: 4.293A pdb=" N SER A 680 " --> pdb=" O CYS A 676 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 682 " --> pdb=" O HIS A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 676 through 682' Processing helix chain 'A' and resid 683 through 686 Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 806 through 813 Processing helix chain 'A' and resid 814 through 817 Processing helix chain 'A' and resid 818 through 846 removed outlier: 3.546A pdb=" N SER A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 899 through 904 removed outlier: 3.945A pdb=" N ASP A 903 " --> pdb=" O GLN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 932 through 945 Processing helix chain 'A' and resid 963 through 974 Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 985 through 999 Processing helix chain 'A' and resid 1000 through 1003 Processing helix chain 'A' and resid 1008 through 1032 removed outlier: 3.620A pdb=" N VAL A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A1028 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1051 through 1098 removed outlier: 3.806A pdb=" N GLU A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 346 through 356 Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.956A pdb=" N PHE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.690A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 524 through 533 removed outlier: 3.608A pdb=" N ASN B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 676 through 682 removed outlier: 4.293A pdb=" N SER B 680 " --> pdb=" O CYS B 676 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 682 " --> pdb=" O HIS B 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 682' Processing helix chain 'B' and resid 683 through 686 Processing helix chain 'B' and resid 687 through 694 Processing helix chain 'B' and resid 797 through 804 Processing helix chain 'B' and resid 806 through 813 Processing helix chain 'B' and resid 814 through 817 Processing helix chain 'B' and resid 818 through 846 removed outlier: 3.546A pdb=" N SER B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 890 Processing helix chain 'B' and resid 899 through 904 removed outlier: 3.946A pdb=" N ASP B 903 " --> pdb=" O GLN B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 918 Processing helix chain 'B' and resid 918 through 923 Processing helix chain 'B' and resid 932 through 945 Processing helix chain 'B' and resid 963 through 974 Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 985 through 999 Processing helix chain 'B' and resid 1000 through 1003 Processing helix chain 'B' and resid 1008 through 1032 removed outlier: 3.620A pdb=" N VAL B1014 " --> pdb=" O ALA B1010 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B1028 " --> pdb=" O ALA B1024 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1048 Processing helix chain 'B' and resid 1051 through 1098 removed outlier: 3.805A pdb=" N GLU B1056 " --> pdb=" O VAL B1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 346 through 356 Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.956A pdb=" N PHE C 393 " --> pdb=" O PHE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.690A pdb=" N LEU C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 466 through 471 Processing helix chain 'C' and resid 489 through 493 Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.608A pdb=" N ASN C 533 " --> pdb=" O THR C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 561 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'C' and resid 676 through 682 removed outlier: 4.293A pdb=" N SER C 680 " --> pdb=" O CYS C 676 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 681 " --> pdb=" O GLN C 677 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET C 682 " --> pdb=" O HIS C 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 676 through 682' Processing helix chain 'C' and resid 683 through 686 Processing helix chain 'C' and resid 687 through 694 Processing helix chain 'C' and resid 797 through 804 Processing helix chain 'C' and resid 806 through 813 Processing helix chain 'C' and resid 814 through 817 Processing helix chain 'C' and resid 818 through 846 removed outlier: 3.546A pdb=" N SER C 844 " --> pdb=" O ASN C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 890 Processing helix chain 'C' and resid 899 through 904 removed outlier: 3.946A pdb=" N ASP C 903 " --> pdb=" O GLN C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 918 Processing helix chain 'C' and resid 918 through 923 Processing helix chain 'C' and resid 932 through 945 Processing helix chain 'C' and resid 963 through 974 Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 985 through 999 Processing helix chain 'C' and resid 1000 through 1003 Processing helix chain 'C' and resid 1008 through 1032 removed outlier: 3.620A pdb=" N VAL C1014 " --> pdb=" O ALA C1010 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C1028 " --> pdb=" O ALA C1024 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C1032 " --> pdb=" O LEU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1048 Processing helix chain 'C' and resid 1051 through 1098 removed outlier: 3.805A pdb=" N GLU C1056 " --> pdb=" O VAL C1052 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.315A pdb=" N ASP A 37 " --> pdb=" O ILE A 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 79 removed outlier: 3.746A pdb=" N GLN A 339 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 91 removed outlier: 6.063A pdb=" N THR A 271 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU A 284 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.506A pdb=" N PHE A 184 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU A 245 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 186 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR A 243 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR A 188 " --> pdb=" O CYS A 241 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS A 241 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA6, first strand: chain 'A' and resid 363 through 366 Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.721A pdb=" N ILE A 636 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 637 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 404 through 408 removed outlier: 3.875A pdb=" N SER A 444 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A 481 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS A 429 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 483 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 427 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS A 485 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 514 removed outlier: 6.442A pdb=" N SER A 553 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS A 506 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG A 551 " --> pdb=" O CYS A 506 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR A 508 " --> pdb=" O PRO A 549 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.756A pdb=" N HIS A 716 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N SER A 753 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N THR A 718 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 760 through 761 removed outlier: 5.757A pdb=" N LEU A 760 " --> pdb=" O THR C 850 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1113 through 1122 removed outlier: 5.908A pdb=" N HIS A1114 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A1142 " --> pdb=" O LYS A1166 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE A1164 " --> pdb=" O ALA A1144 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY A1180 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA A1185 " --> pdb=" O GLY A1180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1113 through 1122 removed outlier: 5.908A pdb=" N HIS A1114 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A1136 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN A 777 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS A1138 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU A1140 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER A 773 " --> pdb=" O GLU A1140 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A1142 " --> pdb=" O LYS A 771 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A 771 " --> pdb=" O VAL A1142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 794 through 796 Processing sheet with id=AB7, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB8, first strand: chain 'A' and resid 959 through 960 removed outlier: 6.744A pdb=" N LYS B 771 " --> pdb=" O VAL B1142 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B1142 " --> pdb=" O LYS B 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER B 773 " --> pdb=" O GLU B1140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU B1140 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS B1138 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN B 777 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B1136 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B1114 " --> pdb=" O TYR B1133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 959 through 960 removed outlier: 6.744A pdb=" N LYS B 771 " --> pdb=" O VAL B1142 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B1142 " --> pdb=" O LYS B 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER B 773 " --> pdb=" O GLU B1140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU B1140 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS B1138 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN B 777 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B1136 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL B1142 " --> pdb=" O LYS B1166 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B1164 " --> pdb=" O ALA B1144 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY B1180 " --> pdb=" O ALA B1185 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA B1185 " --> pdb=" O GLY B1180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1194 through 1197 removed outlier: 4.219A pdb=" N CYS A1156 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN A1155 " --> pdb=" O ASP A1149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.314A pdb=" N ASP B 37 " --> pdb=" O ILE B 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 72 through 79 removed outlier: 3.746A pdb=" N GLN B 339 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 87 through 91 removed outlier: 6.064A pdb=" N THR B 271 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU B 284 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.506A pdb=" N PHE B 184 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU B 245 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 186 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR B 243 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR B 188 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS B 241 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AC7, first strand: chain 'B' and resid 363 through 366 Processing sheet with id=AC8, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.722A pdb=" N ILE B 636 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 637 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.874A pdb=" N SER B 444 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER B 481 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS B 429 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 483 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE B 427 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS B 485 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AD2, first strand: chain 'B' and resid 513 through 514 removed outlier: 6.442A pdb=" N SER B 553 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 506 " --> pdb=" O ARG B 551 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG B 551 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR B 508 " --> pdb=" O PRO B 549 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 722 removed outlier: 6.756A pdb=" N HIS B 716 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N SER B 753 " --> pdb=" O HIS B 716 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N THR B 718 " --> pdb=" O SER B 753 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 794 through 796 Processing sheet with id=AD5, first strand: chain 'B' and resid 849 through 850 Processing sheet with id=AD6, first strand: chain 'B' and resid 959 through 960 removed outlier: 6.744A pdb=" N LYS C 771 " --> pdb=" O VAL C1142 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1142 " --> pdb=" O LYS C 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER C 773 " --> pdb=" O GLU C1140 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU C1140 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS C1138 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 777 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C1136 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR C1133 " --> pdb=" O HIS C1114 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS C1114 " --> pdb=" O TYR C1133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 959 through 960 removed outlier: 6.744A pdb=" N LYS C 771 " --> pdb=" O VAL C1142 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1142 " --> pdb=" O LYS C 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER C 773 " --> pdb=" O GLU C1140 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU C1140 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS C1138 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 777 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C1136 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL C1142 " --> pdb=" O LYS C1166 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE C1164 " --> pdb=" O ALA C1144 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY C1180 " --> pdb=" O ALA C1185 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA C1185 " --> pdb=" O GLY C1180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1194 through 1197 removed outlier: 4.219A pdb=" N CYS B1156 " --> pdb=" O VAL B1197 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN B1155 " --> pdb=" O ASP B1149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 37 through 38 removed outlier: 6.314A pdb=" N ASP C 37 " --> pdb=" O ILE C 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 79 removed outlier: 3.746A pdb=" N GLN C 339 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.063A pdb=" N THR C 271 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU C 284 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.506A pdb=" N PHE C 184 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU C 245 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 186 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR C 243 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TYR C 188 " --> pdb=" O CYS C 241 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS C 241 " --> pdb=" O TYR C 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 156 through 158 Processing sheet with id=AE5, first strand: chain 'C' and resid 363 through 366 Processing sheet with id=AE6, first strand: chain 'C' and resid 377 through 380 removed outlier: 4.722A pdb=" N ILE C 636 " --> pdb=" O VAL C 648 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 637 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 404 through 408 removed outlier: 3.875A pdb=" N SER C 444 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 481 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS C 429 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG C 483 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 427 " --> pdb=" O ARG C 483 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS C 485 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AE9, first strand: chain 'C' and resid 513 through 514 removed outlier: 6.443A pdb=" N SER C 553 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS C 506 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG C 551 " --> pdb=" O CYS C 506 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR C 508 " --> pdb=" O PRO C 549 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 715 through 722 removed outlier: 6.757A pdb=" N HIS C 716 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N SER C 753 " --> pdb=" O HIS C 716 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N THR C 718 " --> pdb=" O SER C 753 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 733 " --> pdb=" O LEU C 729 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 794 through 796 Processing sheet with id=AF3, first strand: chain 'C' and resid 1194 through 1197 removed outlier: 4.219A pdb=" N CYS C1156 " --> pdb=" O VAL C1197 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN C1155 " --> pdb=" O ASP C1149 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 2955 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: 12.60 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 4104 1.27 - 1.42: 7015 1.42 - 1.57: 14783 1.57 - 1.72: 73 1.72 - 1.87: 180 Bond restraints: 26155 Sorted by residual: bond pdb=" C LYS C 487 " pdb=" O LYS C 487 " ideal model delta sigma weight residual 1.236 1.116 0.119 1.22e-02 6.72e+03 9.59e+01 bond pdb=" C LYS B 487 " pdb=" O LYS B 487 " ideal model delta sigma weight residual 1.236 1.117 0.119 1.22e-02 6.72e+03 9.53e+01 bond pdb=" C LYS A 487 " pdb=" O LYS A 487 " ideal model delta sigma weight residual 1.236 1.117 0.119 1.22e-02 6.72e+03 9.52e+01 bond pdb=" C LYS C1013 " pdb=" O LYS C1013 " ideal model delta sigma weight residual 1.236 1.123 0.114 1.24e-02 6.50e+03 8.43e+01 bond pdb=" C LYS B1013 " pdb=" O LYS B1013 " ideal model delta sigma weight residual 1.236 1.123 0.114 1.24e-02 6.50e+03 8.38e+01 ... (remaining 26150 not shown) Histogram of bond angle deviations from ideal: 96.23 - 103.79: 417 103.79 - 111.34: 10640 111.34 - 118.90: 9540 118.90 - 126.46: 14940 126.46 - 134.01: 173 Bond angle restraints: 35710 Sorted by residual: angle pdb=" C ARG A 588 " pdb=" CA ARG A 588 " pdb=" CB ARG A 588 " ideal model delta sigma weight residual 109.60 124.44 -14.84 1.51e+00 4.39e-01 9.66e+01 angle pdb=" C ARG C 588 " pdb=" CA ARG C 588 " pdb=" CB ARG C 588 " ideal model delta sigma weight residual 109.60 124.42 -14.82 1.51e+00 4.39e-01 9.63e+01 angle pdb=" C ARG B 588 " pdb=" CA ARG B 588 " pdb=" CB ARG B 588 " ideal model delta sigma weight residual 109.60 124.41 -14.81 1.51e+00 4.39e-01 9.62e+01 angle pdb=" N VAL B 249 " pdb=" CA VAL B 249 " pdb=" C VAL B 249 " ideal model delta sigma weight residual 111.67 103.22 8.45 9.50e-01 1.11e+00 7.92e+01 angle pdb=" N VAL A 249 " pdb=" CA VAL A 249 " pdb=" C VAL A 249 " ideal model delta sigma weight residual 111.67 103.22 8.45 9.50e-01 1.11e+00 7.92e+01 ... (remaining 35705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 15057 16.75 - 33.51: 674 33.51 - 50.26: 152 50.26 - 67.02: 93 67.02 - 83.77: 27 Dihedral angle restraints: 16003 sinusoidal: 6403 harmonic: 9600 Sorted by residual: dihedral pdb=" CD ARG C 913 " pdb=" NE ARG C 913 " pdb=" CZ ARG C 913 " pdb=" NH1 ARG C 913 " ideal model delta sinusoidal sigma weight residual 0.00 64.47 -64.47 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CD ARG A 913 " pdb=" NE ARG A 913 " pdb=" CZ ARG A 913 " pdb=" NH1 ARG A 913 " ideal model delta sinusoidal sigma weight residual 0.00 64.44 -64.44 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CD ARG B 913 " pdb=" NE ARG B 913 " pdb=" CZ ARG B 913 " pdb=" NH1 ARG B 913 " ideal model delta sinusoidal sigma weight residual 0.00 64.44 -64.44 1 1.00e+01 1.00e-02 5.46e+01 ... (remaining 16000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3644 0.131 - 0.262: 419 0.262 - 0.393: 97 0.393 - 0.525: 10 0.525 - 0.656: 3 Chirality restraints: 4173 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.65e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.63e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.62e+01 ... (remaining 4170 not shown) Planarity restraints: 4629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1410 " -0.139 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG B1410 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG B1410 " -0.104 2.00e-02 2.50e+03 pdb=" N2 NAG B1410 " 0.182 2.00e-02 2.50e+03 pdb=" O7 NAG B1410 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1410 " 0.139 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG C1410 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG C1410 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG C1410 " -0.182 2.00e-02 2.50e+03 pdb=" O7 NAG C1410 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1410 " 0.138 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG A1410 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG A1410 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG A1410 " -0.182 2.00e-02 2.50e+03 pdb=" O7 NAG A1410 " -0.021 2.00e-02 2.50e+03 ... (remaining 4626 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9914 2.89 - 3.39: 22956 3.39 - 3.90: 45052 3.90 - 4.40: 52925 4.40 - 4.90: 85516 Nonbonded interactions: 216363 Sorted by model distance: nonbonded pdb=" NE ARG A1105 " pdb=" OE2 GLU C1097 " model vdw 2.390 2.520 nonbonded pdb=" OE2 GLU B1097 " pdb=" NE ARG C1105 " model vdw 2.390 2.520 nonbonded pdb=" OE2 GLU A1097 " pdb=" NE ARG B1105 " model vdw 2.390 2.520 nonbonded pdb=" O LYS B 145 " pdb=" CB LYS B 145 " model vdw 2.428 2.752 nonbonded pdb=" O LYS A 145 " pdb=" CB LYS A 145 " model vdw 2.428 2.752 ... (remaining 216358 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 'B' and (resid 33 through 365 or (resid 366 and (name N or name CA or nam \ e C or name O or name CB )) or resid 367 through 1215 or resid 1401 through 1413 \ )) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.770 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 74.740 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.015 0.119 26155 Z= 0.989 Angle : 1.595 17.069 35710 Z= 1.072 Chirality : 0.098 0.656 4173 Planarity : 0.020 0.453 4584 Dihedral : 11.683 83.770 9733 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.58 % Favored : 98.23 % Rotamer: Outliers : 1.61 % Allowed : 1.36 % Favored : 97.03 % Cbeta Deviations : 1.53 % 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: 0.53 (0.14), residues: 3219 helix: -0.21 (0.17), residues: 735 sheet: 1.20 (0.19), residues: 615 loop : 0.44 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B1176 HIS 0.005 0.001 HIS C1114 PHE 0.025 0.004 PHE C 184 TYR 0.042 0.006 TYR A 109 ARG 0.012 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 339 time to evaluate : 2.864 Fit side-chains revert: symmetry clash REVERT: A 395 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: A 401 MET cc_start: 0.8424 (ptm) cc_final: 0.8115 (ptm) REVERT: A 931 MET cc_start: 0.8526 (mtt) cc_final: 0.8228 (mtm) REVERT: B 391 ASP cc_start: 0.6522 (t70) cc_final: 0.6151 (t0) REVERT: B 395 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: B 631 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7724 (mmtp) REVERT: B 691 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7612 (ttm110) REVERT: B 931 MET cc_start: 0.8546 (mtt) cc_final: 0.8176 (mtt) REVERT: C 395 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6838 (mt-10) outliers start: 39 outliers final: 11 residues processed: 378 average time/residue: 1.3822 time to fit residues: 605.8118 Evaluate side-chains 222 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 1013 LYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 1013 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.7980 chunk 247 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 296 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 192 GLN A 991 ASN A1076 GLN A1077 GLN A1089 GLN A1114 HIS A1121 ASN B 35 GLN B 192 GLN B 324 GLN B 423 GLN B 991 ASN B1076 GLN B1077 GLN B1089 GLN B1114 HIS B1121 ASN C 35 GLN C 185 GLN C 280 ASN C1076 GLN C1077 GLN C1114 HIS C1137 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26155 Z= 0.217 Angle : 0.609 9.950 35710 Z= 0.323 Chirality : 0.045 0.201 4173 Planarity : 0.004 0.034 4584 Dihedral : 6.540 64.753 4692 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.85 % Allowed : 5.68 % Favored : 92.46 % 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: 0.95 (0.15), residues: 3219 helix: 1.36 (0.20), residues: 738 sheet: 0.70 (0.19), residues: 657 loop : 0.42 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 449 HIS 0.005 0.001 HIS B 678 PHE 0.018 0.002 PHE B 842 TYR 0.016 0.002 TYR B 365 ARG 0.007 0.001 ARG C 913 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 248 time to evaluate : 2.754 Fit side-chains REVERT: A 246 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.6104 (mt-10) REVERT: A 395 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: A 430 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7352 (t70) REVERT: A 448 ASP cc_start: 0.8642 (m-30) cc_final: 0.8405 (m-30) REVERT: A 588 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7680 (mtp85) REVERT: A 931 MET cc_start: 0.8421 (mtt) cc_final: 0.8095 (mtm) REVERT: B 391 ASP cc_start: 0.6776 (t70) cc_final: 0.6304 (t0) REVERT: B 395 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6818 (mt-10) REVERT: B 539 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: B 588 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7189 (mtt180) REVERT: B 682 MET cc_start: 0.7616 (mtp) cc_final: 0.7375 (mtm) REVERT: B 840 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7731 (m-40) REVERT: B 898 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7263 (ttt) REVERT: B 931 MET cc_start: 0.8429 (mtt) cc_final: 0.8113 (mtt) REVERT: C 332 ASP cc_start: 0.8048 (p0) cc_final: 0.7787 (p0) REVERT: C 395 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6923 (mt-10) REVERT: C 539 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7606 (mp10) outliers start: 45 outliers final: 10 residues processed: 279 average time/residue: 1.4792 time to fit residues: 478.1786 Evaluate side-chains 216 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 81 optimal weight: 0.0270 chunk 297 optimal weight: 3.9990 chunk 321 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 GLN B 35 GLN B 324 GLN B 703 ASN B1012 GLN B1023 GLN B1076 GLN C 35 GLN C 423 GLN C 703 ASN C1137 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 26155 Z= 0.396 Angle : 0.663 9.321 35710 Z= 0.348 Chirality : 0.048 0.168 4173 Planarity : 0.005 0.051 4584 Dihedral : 6.241 59.489 4667 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.64 % Allowed : 6.51 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.58 (0.14), residues: 3219 helix: 1.15 (0.19), residues: 774 sheet: 0.32 (0.18), residues: 696 loop : 0.18 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 449 HIS 0.005 0.001 HIS A 268 PHE 0.023 0.002 PHE B 842 TYR 0.018 0.002 TYR B 500 ARG 0.007 0.001 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 198 time to evaluate : 2.852 Fit side-chains REVERT: A 246 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: A 395 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 430 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7267 (t70) REVERT: A 588 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7798 (mtt180) REVERT: A 606 ASP cc_start: 0.8249 (t0) cc_final: 0.7914 (t0) REVERT: A 833 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7595 (mtm-85) REVERT: A 840 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7537 (m110) REVERT: A 931 MET cc_start: 0.8551 (mtt) cc_final: 0.8165 (mtm) REVERT: B 386 ASP cc_start: 0.7975 (m-30) cc_final: 0.7774 (m-30) REVERT: B 539 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: B 588 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7732 (mtt180) REVERT: B 840 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7800 (m-40) REVERT: B 913 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6257 (mmp-170) REVERT: B 931 MET cc_start: 0.8573 (mtt) cc_final: 0.8194 (mtt) REVERT: C 147 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: C 395 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: C 525 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7052 (mp10) REVERT: C 539 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: C 905 MET cc_start: 0.6785 (mtp) cc_final: 0.6571 (mtp) REVERT: C 1140 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7439 (tt0) outliers start: 64 outliers final: 20 residues processed: 240 average time/residue: 1.3969 time to fit residues: 388.4895 Evaluate side-chains 218 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1140 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 316 optimal weight: 0.0470 chunk 155 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1012 GLN ** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN B 324 GLN B 703 ASN B1023 GLN B1076 GLN C 35 GLN C 703 ASN C1012 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26155 Z= 0.240 Angle : 0.559 9.938 35710 Z= 0.295 Chirality : 0.044 0.212 4173 Planarity : 0.004 0.037 4584 Dihedral : 5.877 59.814 4667 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.18 % Allowed : 7.50 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.68 (0.14), residues: 3219 helix: 1.48 (0.19), residues: 756 sheet: 0.29 (0.18), residues: 696 loop : 0.17 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 449 HIS 0.013 0.001 HIS C 678 PHE 0.021 0.002 PHE B 842 TYR 0.018 0.001 TYR C 198 ARG 0.004 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 191 time to evaluate : 2.706 Fit side-chains REVERT: A 246 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6172 (mp0) REVERT: A 606 ASP cc_start: 0.8233 (t0) cc_final: 0.7894 (t0) REVERT: A 682 MET cc_start: 0.7514 (mtp) cc_final: 0.7219 (mtm) REVERT: A 840 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7478 (m110) REVERT: A 931 MET cc_start: 0.8523 (mtt) cc_final: 0.8173 (mtm) REVERT: B 588 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7656 (mtt180) REVERT: B 840 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7681 (m-40) REVERT: B 913 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6143 (mmp-170) REVERT: B 931 MET cc_start: 0.8502 (mtt) cc_final: 0.8092 (mtt) REVERT: C 395 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: C 539 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: C 1140 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7361 (tt0) outliers start: 53 outliers final: 17 residues processed: 225 average time/residue: 1.4161 time to fit residues: 368.8461 Evaluate side-chains 213 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1140 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 5.9990 chunk 179 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 703 ASN A1076 GLN A1193 ASN B 35 GLN B 185 GLN B 678 HIS B 703 ASN B1023 GLN B1076 GLN B1161 ASN C 703 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 26155 Z= 0.507 Angle : 0.690 12.843 35710 Z= 0.359 Chirality : 0.050 0.278 4173 Planarity : 0.005 0.045 4584 Dihedral : 6.178 59.380 4660 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.97 % Allowed : 7.62 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.34 (0.14), residues: 3219 helix: 1.00 (0.19), residues: 774 sheet: 0.15 (0.18), residues: 678 loop : 0.01 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 449 HIS 0.014 0.002 HIS C 678 PHE 0.022 0.003 PHE B 842 TYR 0.020 0.002 TYR B 500 ARG 0.007 0.001 ARG C 688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 192 time to evaluate : 2.666 Fit side-chains REVERT: A 147 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: A 430 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7308 (t70) REVERT: A 539 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: A 588 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7917 (mtt180) REVERT: A 606 ASP cc_start: 0.8250 (t0) cc_final: 0.7930 (t0) REVERT: A 840 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7541 (m110) REVERT: A 931 MET cc_start: 0.8596 (mtt) cc_final: 0.8204 (mtm) REVERT: A 1140 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: B 395 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: B 840 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7776 (m-40) REVERT: B 898 MET cc_start: 0.7621 (ttt) cc_final: 0.7142 (ttt) REVERT: B 931 MET cc_start: 0.8642 (mtt) cc_final: 0.8306 (mtt) REVERT: C 147 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: C 395 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: C 525 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7067 (mp10) REVERT: C 539 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: C 840 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7527 (m-40) REVERT: C 1140 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7422 (tt0) outliers start: 72 outliers final: 22 residues processed: 238 average time/residue: 1.4223 time to fit residues: 390.9018 Evaluate side-chains 217 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 TYR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1140 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 2.9990 chunk 284 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A1161 ASN B 35 GLN B 703 ASN B1023 GLN B1076 GLN B1161 ASN ** C 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26155 Z= 0.284 Angle : 0.586 12.711 35710 Z= 0.308 Chirality : 0.045 0.235 4173 Planarity : 0.004 0.044 4584 Dihedral : 5.782 59.474 4660 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.47 % Allowed : 8.94 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.44 (0.14), residues: 3219 helix: 1.35 (0.19), residues: 756 sheet: 0.03 (0.18), residues: 681 loop : 0.03 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 449 HIS 0.014 0.001 HIS C 678 PHE 0.020 0.002 PHE B 842 TYR 0.019 0.002 TYR C 198 ARG 0.004 0.000 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 194 time to evaluate : 3.122 Fit side-chains revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: A 588 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7865 (mtt180) REVERT: A 606 ASP cc_start: 0.8245 (t0) cc_final: 0.7930 (t0) REVERT: A 840 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7466 (m110) REVERT: A 931 MET cc_start: 0.8563 (mtt) cc_final: 0.8239 (mtm) REVERT: B 840 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7741 (m-40) REVERT: B 913 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6117 (mmp-170) REVERT: B 931 MET cc_start: 0.8541 (mtt) cc_final: 0.8156 (mtt) REVERT: C 147 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: C 360 MET cc_start: 0.8262 (mtp) cc_final: 0.7717 (mtp) REVERT: C 525 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7006 (mp10) REVERT: C 539 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: C 1140 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7360 (tt0) outliers start: 60 outliers final: 26 residues processed: 231 average time/residue: 1.4338 time to fit residues: 382.3407 Evaluate side-chains 220 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 TYR Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 266 optimal weight: 0.3980 chunk 176 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN B 35 GLN B 703 ASN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 703 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26155 Z= 0.198 Angle : 0.531 11.150 35710 Z= 0.280 Chirality : 0.043 0.214 4173 Planarity : 0.004 0.041 4584 Dihedral : 5.294 58.580 4657 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.06 % Allowed : 9.84 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.56 (0.14), residues: 3219 helix: 1.61 (0.19), residues: 762 sheet: -0.03 (0.18), residues: 684 loop : 0.09 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 449 HIS 0.012 0.001 HIS C 678 PHE 0.020 0.001 PHE C 184 TYR 0.017 0.001 TYR C 198 ARG 0.004 0.000 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 190 time to evaluate : 2.949 Fit side-chains revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: A 430 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7231 (t70) REVERT: A 588 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7769 (mtt180) REVERT: A 606 ASP cc_start: 0.8233 (t0) cc_final: 0.7914 (t0) REVERT: A 840 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7404 (m110) REVERT: A 931 MET cc_start: 0.8554 (mtt) cc_final: 0.8203 (mtm) REVERT: A 1027 LYS cc_start: 0.8183 (mttp) cc_final: 0.7934 (tttp) REVERT: B 539 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: B 630 ASP cc_start: 0.7410 (p0) cc_final: 0.7116 (p0) REVERT: B 840 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7710 (m-40) REVERT: B 913 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6152 (mmp-170) REVERT: B 931 MET cc_start: 0.8489 (mtt) cc_final: 0.8137 (mtm) REVERT: C 147 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: C 525 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: C 539 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: C 840 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7466 (m-40) outliers start: 50 outliers final: 19 residues processed: 224 average time/residue: 1.3942 time to fit residues: 362.2660 Evaluate side-chains 213 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 TYR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 913 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 200 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A1076 GLN A1193 ASN B 35 GLN B 703 ASN B1076 GLN C 339 GLN C 703 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 26155 Z= 0.421 Angle : 0.648 14.114 35710 Z= 0.337 Chirality : 0.048 0.259 4173 Planarity : 0.005 0.045 4584 Dihedral : 5.629 58.659 4651 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.18 % Allowed : 10.26 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.41 (0.14), residues: 3219 helix: 1.44 (0.19), residues: 738 sheet: -0.14 (0.18), residues: 696 loop : 0.05 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 449 HIS 0.017 0.002 HIS C 678 PHE 0.019 0.002 PHE B 842 TYR 0.020 0.002 TYR C 198 ARG 0.005 0.001 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 184 time to evaluate : 2.858 Fit side-chains revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 539 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: A 588 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7907 (mtt180) REVERT: A 606 ASP cc_start: 0.8259 (t0) cc_final: 0.7956 (t0) REVERT: A 840 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7506 (m110) REVERT: A 931 MET cc_start: 0.8585 (mtt) cc_final: 0.8236 (mtm) REVERT: B 395 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: B 539 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: B 630 ASP cc_start: 0.7315 (p0) cc_final: 0.7039 (p0) REVERT: B 840 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7757 (m-40) REVERT: B 931 MET cc_start: 0.8601 (mtt) cc_final: 0.8220 (mtt) REVERT: C 147 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: C 360 MET cc_start: 0.8287 (mtp) cc_final: 0.7812 (mtp) REVERT: C 395 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: C 539 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: C 840 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7563 (m-40) outliers start: 53 outliers final: 26 residues processed: 221 average time/residue: 1.4161 time to fit residues: 361.5026 Evaluate side-chains 217 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 TYR Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 277 optimal weight: 0.7980 chunk 292 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A1077 GLN B 35 GLN B 703 ASN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN ** C 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26155 Z= 0.195 Angle : 0.539 13.488 35710 Z= 0.283 Chirality : 0.043 0.215 4173 Planarity : 0.004 0.042 4584 Dihedral : 5.159 57.648 4651 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.52 % Allowed : 11.08 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.52 (0.14), residues: 3219 helix: 1.68 (0.19), residues: 747 sheet: -0.13 (0.18), residues: 717 loop : 0.06 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 449 HIS 0.010 0.001 HIS C 678 PHE 0.019 0.001 PHE C 184 TYR 0.015 0.001 TYR C 198 ARG 0.004 0.000 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: A 426 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: A 588 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7891 (mtt180) REVERT: A 606 ASP cc_start: 0.8227 (t0) cc_final: 0.7927 (t0) REVERT: A 840 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7416 (m110) REVERT: A 913 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6164 (mmp-170) REVERT: A 931 MET cc_start: 0.8522 (mtt) cc_final: 0.8209 (mtm) REVERT: A 1027 LYS cc_start: 0.8180 (mttp) cc_final: 0.7940 (tttp) REVERT: B 539 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: B 585 LYS cc_start: 0.8159 (mtpm) cc_final: 0.7925 (mtpt) REVERT: B 630 ASP cc_start: 0.7349 (p0) cc_final: 0.7102 (p0) REVERT: B 840 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7702 (m-40) REVERT: B 905 MET cc_start: 0.6313 (mtp) cc_final: 0.6012 (mtp) REVERT: B 931 MET cc_start: 0.8510 (mtt) cc_final: 0.8106 (mtt) REVERT: C 147 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: C 539 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7663 (mp10) outliers start: 37 outliers final: 18 residues processed: 211 average time/residue: 1.4278 time to fit residues: 349.0893 Evaluate side-chains 214 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 TYR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 953 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 215 optimal weight: 0.0870 chunk 325 optimal weight: 0.4980 chunk 299 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN B 35 GLN B 703 ASN B1076 GLN C 678 HIS C 703 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 26155 Z= 0.284 Angle : 0.573 14.319 35710 Z= 0.300 Chirality : 0.044 0.228 4173 Planarity : 0.004 0.042 4584 Dihedral : 5.240 57.566 4651 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.81 % Allowed : 10.83 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.51 (0.14), residues: 3219 helix: 1.71 (0.19), residues: 741 sheet: -0.12 (0.18), residues: 708 loop : 0.03 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 449 HIS 0.010 0.001 HIS C 678 PHE 0.019 0.002 PHE C 184 TYR 0.017 0.002 TYR B1133 ARG 0.004 0.000 ARG A1195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 189 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: A 426 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: A 588 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7888 (mtt180) REVERT: A 606 ASP cc_start: 0.8246 (t0) cc_final: 0.7938 (t0) REVERT: A 840 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7418 (m110) REVERT: A 913 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6165 (mmp-170) REVERT: A 931 MET cc_start: 0.8540 (mtt) cc_final: 0.8217 (mtm) REVERT: B 539 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: B 630 ASP cc_start: 0.7347 (p0) cc_final: 0.7102 (p0) REVERT: B 840 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7727 (m-40) REVERT: B 905 MET cc_start: 0.6368 (mtp) cc_final: 0.6083 (mtp) REVERT: B 931 MET cc_start: 0.8521 (mtt) cc_final: 0.8132 (mtt) REVERT: C 147 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: C 539 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: C 840 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7490 (m-40) outliers start: 44 outliers final: 26 residues processed: 218 average time/residue: 1.4443 time to fit residues: 364.0984 Evaluate side-chains 222 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 TYR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 986 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN B 35 GLN B 703 ASN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107176 restraints weight = 29486.841| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.72 r_work: 0.3198 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26155 Z= 0.243 Angle : 0.551 14.003 35710 Z= 0.289 Chirality : 0.044 0.219 4173 Planarity : 0.004 0.042 4584 Dihedral : 5.135 57.253 4651 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.52 % Allowed : 11.20 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.54 (0.14), residues: 3219 helix: 1.77 (0.19), residues: 741 sheet: -0.11 (0.18), residues: 708 loop : 0.04 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 449 HIS 0.017 0.001 HIS C 678 PHE 0.020 0.002 PHE C 184 TYR 0.016 0.001 TYR B1133 ARG 0.005 0.000 ARG A1195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7704.06 seconds wall clock time: 139 minutes 5.11 seconds (8345.11 seconds total)