Starting phenix.real_space_refine on Sun Mar 24 14:43:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7o_12751/03_2024/7o7o_12751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7o_12751/03_2024/7o7o_12751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7o_12751/03_2024/7o7o_12751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7o_12751/03_2024/7o7o_12751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7o_12751/03_2024/7o7o_12751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7o_12751/03_2024/7o7o_12751.pdb" } resolution = 4.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 182 5.16 5 C 27066 2.51 5 N 7070 2.21 5 O 8324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A GLU 908": "OE1" <-> "OE2" Residue "A GLU 913": "OE1" <-> "OE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "A GLU 974": "OE1" <-> "OE2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1137": "OE1" <-> "OE2" Residue "A GLU 1165": "OE1" <-> "OE2" Residue "A GLU 1173": "OE1" <-> "OE2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A GLU 1205": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B GLU 1137": "OE1" <-> "OE2" Residue "B GLU 1184": "OE1" <-> "OE2" Residue "B PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1198": "OE1" <-> "OE2" Residue "B GLU 1454": "OE1" <-> "OE2" Residue "B GLU 1462": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 840": "OE1" <-> "OE2" Residue "C GLU 881": "OE1" <-> "OE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C GLU 913": "OE1" <-> "OE2" Residue "C GLU 926": "OE1" <-> "OE2" Residue "C GLU 974": "OE1" <-> "OE2" Residue "C GLU 992": "OE1" <-> "OE2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C GLU 1096": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C GLU 1165": "OE1" <-> "OE2" Residue "C GLU 1173": "OE1" <-> "OE2" Residue "C GLU 1198": "OE1" <-> "OE2" Residue "C GLU 1205": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D GLU 795": "OE1" <-> "OE2" Residue "D GLU 930": "OE1" <-> "OE2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "D GLU 1184": "OE1" <-> "OE2" Residue "D PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1198": "OE1" <-> "OE2" Residue "D GLU 1454": "OE1" <-> "OE2" Residue "D GLU 1462": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42642 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "B" Number of atoms: 11004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11004 Classifications: {'peptide': 1410} Link IDs: {'PTRANS': 74, 'TRANS': 1335} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "D" Number of atoms: 11004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11004 Classifications: {'peptide': 1410} Link IDs: {'PTRANS': 74, 'TRANS': 1335} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 21.63, per 1000 atoms: 0.51 Number of scatterers: 42642 At special positions: 0 Unit cell: (210.447, 162.285, 194.742, 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 182 16.00 O 8324 8.00 N 7070 7.00 C 27066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 86 " distance=2.02 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.04 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.03 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.06 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.04 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 771 " distance=2.04 Simple disulfide: pdb=" SG CYS B 642 " - pdb=" SG CYS B 689 " distance=2.04 Simple disulfide: pdb=" SG CYS B 821 " - pdb=" SG CYS B 849 " distance=2.04 Simple disulfide: pdb=" SG CYS B 847 " - pdb=" SG CYS B 883 " distance=2.05 Simple disulfide: pdb=" SG CYS B 921 " - pdb=" SG CYS B1321 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1127 " distance=2.04 Simple disulfide: pdb=" SG CYS B1352 " - pdb=" SG CYS B1467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.02 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS D 278 " distance=2.05 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.04 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.03 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.03 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.03 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.06 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.04 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.04 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.04 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.04 Simple disulfide: pdb=" SG CYS D 847 " - pdb=" SG CYS D 883 " distance=2.05 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " distance=2.04 Simple disulfide: pdb=" SG CYS D1352 " - pdb=" SG CYS D1467 " 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 247 " " NAG A2003 " - " ASN A 410 " " NAG A2004 " - " ASN A 869 " " NAG A2005 " - " ASN A 991 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 869 " " NAG B2004 " - " ASN B 991 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 247 " " NAG C2003 " - " ASN C 410 " " NAG C2004 " - " ASN C 869 " " NAG C2005 " - " ASN C 991 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 869 " " NAG D2004 " - " ASN D 991 " " NAG E 1 " - " ASN A 70 " " NAG F 1 " - " ASN A 396 " " NAG G 1 " - " ASN B 247 " " NAG H 1 " - " ASN B 396 " " NAG I 1 " - " ASN B 410 " " NAG J 1 " - " ASN B1424 " " NAG K 1 " - " ASN C 70 " " NAG L 1 " - " ASN C 396 " " NAG M 1 " - " ASN D 247 " " NAG N 1 " - " ASN D 396 " " NAG O 1 " - " ASN D 410 " " NAG P 1 " - " ASN D1424 " Time building additional restraints: 18.55 Conformation dependent library (CDL) restraints added in 8.3 seconds 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10092 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 16.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 953 through 965 removed outlier: 6.200A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1205 through 1217 removed outlier: 4.191A pdb=" N THR A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 removed outlier: 3.529A pdb=" N LEU B 670 " --> pdb=" O MET B 666 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 671 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 962 removed outlier: 6.449A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 958 through 962' Processing helix chain 'B' and resid 973 through 993 removed outlier: 4.556A pdb=" N MET B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) Proline residue: B 982 - end of helix removed outlier: 4.475A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR B 989 " --> pdb=" O TYR B 985 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 990 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 992 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 993 " --> pdb=" O TYR B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 removed outlier: 3.933A pdb=" N GLY B1006 " --> pdb=" O SER B1002 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN B1013 " --> pdb=" O ASN B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1052 removed outlier: 4.281A pdb=" N LYS B1047 " --> pdb=" O ALA B1043 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B1048 " --> pdb=" O PHE B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1073 removed outlier: 3.653A pdb=" N ALA B1066 " --> pdb=" O HIS B1062 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B1073 " --> pdb=" O TRP B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1111 removed outlier: 4.121A pdb=" N THR B1106 " --> pdb=" O SER B1102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B1108 " --> pdb=" O TYR B1104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B1111 " --> pdb=" O ILE B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1137 Processing helix chain 'B' and resid 1144 through 1157 removed outlier: 3.664A pdb=" N ALA B1148 " --> pdb=" O VAL B1144 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B1151 " --> pdb=" O LYS B1147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B1152 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B1154 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B1156 " --> pdb=" O TYR B1152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA B1157 " --> pdb=" O ALA B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1172 removed outlier: 3.501A pdb=" N GLU B1165 " --> pdb=" O ASP B1161 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B1168 " --> pdb=" O LYS B1164 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B1169 " --> pdb=" O GLU B1165 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B1170 " --> pdb=" O VAL B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1217 removed outlier: 3.591A pdb=" N TYR B1211 " --> pdb=" O GLU B1207 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B1217 " --> pdb=" O LEU B1213 " (cutoff:3.500A) Processing helix chain 'B' and resid 1225 through 1241 removed outlier: 4.061A pdb=" N THR B1229 " --> pdb=" O SER B1225 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B1231 " --> pdb=" O ASP B1227 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN B1233 " --> pdb=" O THR B1229 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B1236 " --> pdb=" O THR B1232 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP B1237 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B1238 " --> pdb=" O ILE B1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1268 removed outlier: 5.084A pdb=" N VAL B1255 " --> pdb=" O THR B1251 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B1256 " --> pdb=" O GLN B1252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B1258 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS B1259 " --> pdb=" O VAL B1255 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B1260 " --> pdb=" O VAL B1256 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B1261 " --> pdb=" O ALA B1257 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER B1262 " --> pdb=" O LEU B1258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B1263 " --> pdb=" O HIS B1259 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR B1264 " --> pdb=" O ALA B1260 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY B1265 " --> pdb=" O LEU B1261 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA B1266 " --> pdb=" O SER B1262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1294 through 1297 No H-bonds generated for 'chain 'B' and resid 1294 through 1297' Processing helix chain 'B' and resid 1393 through 1400 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 602 through 607 Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 666 through 673 Processing helix chain 'C' and resid 953 through 965 removed outlier: 6.200A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix Processing helix chain 'C' and resid 998 through 1017 Processing helix chain 'C' and resid 1039 through 1055 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1098 through 1111 Processing helix chain 'C' and resid 1119 through 1137 Processing helix chain 'C' and resid 1144 through 1157 Processing helix chain 'C' and resid 1160 through 1172 Processing helix chain 'C' and resid 1205 through 1217 removed outlier: 4.191A pdb=" N THR C1209 " --> pdb=" O GLU C1205 " (cutoff:3.500A) Processing helix chain 'C' and resid 1225 through 1241 Processing helix chain 'C' and resid 1251 through 1268 Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 602 through 607 Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 666 through 673 removed outlier: 3.529A pdb=" N LEU D 670 " --> pdb=" O MET D 666 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 671 " --> pdb=" O TYR D 667 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET D 673 " --> pdb=" O PHE D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 962 removed outlier: 6.449A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 958 through 962' Processing helix chain 'D' and resid 973 through 993 removed outlier: 4.905A pdb=" N MET D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL D 978 " --> pdb=" O GLU D 974 " (cutoff:3.500A) Proline residue: D 982 - end of helix removed outlier: 4.475A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 986 " --> pdb=" O PRO D 982 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR D 989 " --> pdb=" O TYR D 985 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN D 991 " --> pdb=" O LEU D 987 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU D 992 " --> pdb=" O ASP D 988 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 993 " --> pdb=" O TYR D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 removed outlier: 3.933A pdb=" N GLY D1006 " --> pdb=" O SER D1002 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN D1013 " --> pdb=" O ASN D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1052 removed outlier: 4.281A pdb=" N LYS D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR D1048 " --> pdb=" O PHE D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1073 removed outlier: 3.653A pdb=" N ALA D1066 " --> pdb=" O HIS D1062 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG D1073 " --> pdb=" O TRP D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1111 removed outlier: 4.121A pdb=" N THR D1106 " --> pdb=" O SER D1102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D1108 " --> pdb=" O TYR D1104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D1111 " --> pdb=" O ILE D1107 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1137 Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 3.664A pdb=" N ALA D1148 " --> pdb=" O VAL D1144 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA D1151 " --> pdb=" O LYS D1147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D1152 " --> pdb=" O ALA D1148 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D1154 " --> pdb=" O LEU D1150 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D1156 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA D1157 " --> pdb=" O ALA D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1172 removed outlier: 3.501A pdb=" N GLU D1165 " --> pdb=" O ASP D1161 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS D1168 " --> pdb=" O LYS D1164 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D1169 " --> pdb=" O GLU D1165 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1217 removed outlier: 3.591A pdb=" N TYR D1211 " --> pdb=" O GLU D1207 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D1217 " --> pdb=" O LEU D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 4.061A pdb=" N THR D1229 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D1231 " --> pdb=" O ASP D1227 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D1233 " --> pdb=" O THR D1229 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D1236 " --> pdb=" O THR D1232 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP D1237 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D1238 " --> pdb=" O ILE D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1268 removed outlier: 5.084A pdb=" N VAL D1255 " --> pdb=" O THR D1251 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL D1256 " --> pdb=" O GLN D1252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D1258 " --> pdb=" O THR D1254 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA D1260 " --> pdb=" O VAL D1256 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D1261 " --> pdb=" O ALA D1257 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER D1262 " --> pdb=" O LEU D1258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS D1263 " --> pdb=" O HIS D1259 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR D1264 " --> pdb=" O ALA D1260 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D1265 " --> pdb=" O LEU D1261 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA D1266 " --> pdb=" O SER D1262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D1267 " --> pdb=" O LYS D1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' Processing helix chain 'D' and resid 1393 through 1400 482 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.78 Time building geometry restraints manager: 19.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.07: 4 1.07 - 1.28: 7076 1.28 - 1.48: 17733 1.48 - 1.69: 18491 1.69 - 1.90: 270 Bond restraints: 43574 Sorted by residual: bond pdb=" C LEU C 54 " pdb=" N ASN C 55 " ideal model delta sigma weight residual 1.330 0.861 0.469 1.32e-02 5.74e+03 1.26e+03 bond pdb=" C LEU A 54 " pdb=" N ASN A 55 " ideal model delta sigma weight residual 1.330 0.861 0.469 1.32e-02 5.74e+03 1.26e+03 bond pdb=" C VAL D 978 " pdb=" N LEU D 979 " ideal model delta sigma weight residual 1.334 1.606 -0.271 1.20e-02 6.94e+03 5.11e+02 bond pdb=" C VAL A 868 " pdb=" N ASN A 869 " ideal model delta sigma weight residual 1.330 1.049 0.281 1.37e-02 5.33e+03 4.21e+02 bond pdb=" C VAL C 868 " pdb=" N ASN C 869 " ideal model delta sigma weight residual 1.330 1.049 0.281 1.37e-02 5.33e+03 4.21e+02 ... (remaining 43569 not shown) Histogram of bond angle deviations from ideal: 94.14 - 104.02: 742 104.02 - 113.91: 25472 113.91 - 123.79: 31254 123.79 - 133.67: 1680 133.67 - 143.56: 56 Bond angle restraints: 59204 Sorted by residual: angle pdb=" O LEU D 990 " pdb=" C LEU D 990 " pdb=" N ASN D 991 " ideal model delta sigma weight residual 122.07 143.56 -21.49 1.03e+00 9.43e-01 4.35e+02 angle pdb=" O LEU B 990 " pdb=" C LEU B 990 " pdb=" N ASN B 991 " ideal model delta sigma weight residual 122.07 143.56 -21.49 1.03e+00 9.43e-01 4.35e+02 angle pdb=" CA LEU D 990 " pdb=" C LEU D 990 " pdb=" N ASN D 991 " ideal model delta sigma weight residual 117.07 95.96 21.11 1.14e+00 7.69e-01 3.43e+02 angle pdb=" CA LEU B 990 " pdb=" C LEU B 990 " pdb=" N ASN B 991 " ideal model delta sigma weight residual 117.07 95.96 21.11 1.14e+00 7.69e-01 3.43e+02 angle pdb=" C LEU D 990 " pdb=" N ASN D 991 " pdb=" CA ASN D 991 " ideal model delta sigma weight residual 122.09 94.14 27.95 1.79e+00 3.12e-01 2.44e+02 ... (remaining 59199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 24510 21.16 - 42.32: 2113 42.32 - 63.48: 297 63.48 - 84.64: 90 84.64 - 105.80: 30 Dihedral angle restraints: 27040 sinusoidal: 11372 harmonic: 15668 Sorted by residual: dihedral pdb=" CB CYS C 847 " pdb=" SG CYS C 847 " pdb=" SG CYS C 883 " pdb=" CB CYS C 883 " ideal model delta sinusoidal sigma weight residual 93.00 172.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS A 847 " pdb=" SG CYS A 847 " pdb=" SG CYS A 883 " pdb=" CB CYS A 883 " ideal model delta sinusoidal sigma weight residual 93.00 172.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" C GLU A 908 " pdb=" N GLU A 908 " pdb=" CA GLU A 908 " pdb=" CB GLU A 908 " ideal model delta harmonic sigma weight residual -122.60 -144.21 21.61 0 2.50e+00 1.60e-01 7.47e+01 ... (remaining 27037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 6791 0.168 - 0.336: 93 0.336 - 0.504: 12 0.504 - 0.672: 2 0.672 - 0.840: 2 Chirality restraints: 6900 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.55e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.55e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.57e+02 ... (remaining 6897 not shown) Planarity restraints: 7584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG K 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG E 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG L 1 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.137 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.137 2.00e-02 2.50e+03 ... (remaining 7581 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 117 2.23 - 2.90: 18831 2.90 - 3.57: 69238 3.57 - 4.23: 105783 4.23 - 4.90: 160190 Nonbonded interactions: 354159 Sorted by model distance: nonbonded pdb=" SG CYS B 972 " pdb=" CD GLN B 975 " model vdw 1.564 3.630 nonbonded pdb=" SG CYS D 972 " pdb=" CD GLN D 975 " model vdw 1.659 3.630 nonbonded pdb=" OD1 ASN D 976 " pdb=" NH1 ARG D1014 " model vdw 1.960 2.520 nonbonded pdb=" OG1 THR B 915 " pdb=" O THR B1326 " model vdw 1.992 2.440 nonbonded pdb=" OG1 THR D 915 " pdb=" O THR D1326 " model vdw 1.992 2.440 ... (remaining 354154 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' and (resid 26 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 1337 or resid 2002 through 2005)) selection = (chain 'B' and (resid 26 through 695 or resid 730 through 1337 or resid 2001 thr \ ough 2004)) selection = (chain 'C' and (resid 26 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 1337 or resid 2002 through 2005)) selection = (chain 'D' and (resid 26 through 695 or resid 730 through 1337 or resid 2001 thr \ ough 2004)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.060 Check model and map are aligned: 0.620 Set scattering table: 0.360 Process input model: 103.190 Find NCS groups from input model: 3.690 Set up NCS constraints: 0.450 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.011 0.469 43574 Z= 0.708 Angle : 1.239 27.950 59204 Z= 0.716 Chirality : 0.063 0.840 6900 Planarity : 0.018 0.305 7554 Dihedral : 16.355 105.802 16810 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.47 % Allowed : 17.39 % Favored : 82.15 % Rotamer: Outliers : 0.43 % Allowed : 5.89 % Favored : 93.68 % Cbeta Deviations : 0.10 % 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: -5.42 (0.09), residues: 5360 helix: -2.94 (0.12), residues: 810 sheet: -3.33 (0.11), residues: 1496 loop : -4.08 (0.09), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 741 HIS 0.012 0.002 HIS D 460 PHE 0.033 0.003 PHE D1389 TYR 0.035 0.003 TYR D1418 ARG 0.013 0.001 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 717 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9489 (mp) cc_final: 0.9289 (mp) REVERT: A 55 ASN cc_start: 0.6602 (p0) cc_final: 0.5206 (t0) REVERT: A 93 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7815 (mmtp) REVERT: A 151 MET cc_start: 0.9018 (ttm) cc_final: 0.8258 (tpp) REVERT: A 166 TYR cc_start: 0.7987 (p90) cc_final: 0.7590 (p90) REVERT: A 192 PHE cc_start: 0.7763 (t80) cc_final: 0.7421 (t80) REVERT: A 215 THR cc_start: 0.8867 (t) cc_final: 0.8493 (m) REVERT: A 368 GLN cc_start: 0.9193 (tt0) cc_final: 0.8991 (tm-30) REVERT: A 977 MET cc_start: 0.8244 (mmp) cc_final: 0.7859 (mmm) REVERT: A 1015 GLN cc_start: 0.9287 (tp40) cc_final: 0.8528 (tp40) REVERT: A 1065 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8264 (tp-100) REVERT: A 1086 LEU cc_start: 0.7567 (tp) cc_final: 0.7212 (tp) REVERT: A 1122 ARG cc_start: 0.9059 (ttp-110) cc_final: 0.8797 (tmm-80) REVERT: B 169 ASP cc_start: 0.9112 (t0) cc_final: 0.8462 (t70) REVERT: B 194 LEU cc_start: 0.9239 (tp) cc_final: 0.9014 (tp) REVERT: B 237 LYS cc_start: 0.9132 (mmpt) cc_final: 0.8892 (mmmt) REVERT: B 297 HIS cc_start: 0.8818 (t70) cc_final: 0.8597 (m90) REVERT: B 366 PHE cc_start: 0.9161 (m-10) cc_final: 0.8948 (m-10) REVERT: B 393 TYR cc_start: 0.8782 (t80) cc_final: 0.8340 (t80) REVERT: B 410 ASN cc_start: 0.5906 (OUTLIER) cc_final: 0.5440 (t0) REVERT: B 569 ASP cc_start: 0.8370 (t0) cc_final: 0.8107 (t0) REVERT: B 916 PHE cc_start: 0.8999 (m-80) cc_final: 0.8707 (m-80) REVERT: B 960 GLN cc_start: 0.8166 (mp10) cc_final: 0.7776 (mt0) REVERT: B 1003 LYS cc_start: 0.8527 (tptt) cc_final: 0.8275 (tptt) REVERT: B 1132 TRP cc_start: 0.7224 (t-100) cc_final: 0.7003 (t-100) REVERT: B 1213 LEU cc_start: 0.9513 (tp) cc_final: 0.9296 (tp) REVERT: B 1297 ARG cc_start: 0.8889 (tmm-80) cc_final: 0.8615 (tmm-80) REVERT: B 1298 LEU cc_start: 0.9499 (pt) cc_final: 0.9255 (pt) REVERT: B 1325 GLN cc_start: 0.8783 (pp30) cc_final: 0.8565 (tm-30) REVERT: B 1328 LEU cc_start: 0.9356 (tt) cc_final: 0.8867 (tt) REVERT: B 1330 TYR cc_start: 0.9120 (p90) cc_final: 0.8752 (p90) REVERT: B 1393 LYS cc_start: 0.9088 (tmmt) cc_final: 0.8719 (tptt) REVERT: B 1397 LYS cc_start: 0.9621 (pptt) cc_final: 0.8469 (pttm) REVERT: B 1451 ASP cc_start: 0.3496 (OUTLIER) cc_final: 0.2555 (p0) REVERT: C 34 LEU cc_start: 0.9490 (mp) cc_final: 0.9290 (mp) REVERT: C 55 ASN cc_start: 0.6605 (p0) cc_final: 0.5208 (t0) REVERT: C 93 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7810 (mmtp) REVERT: C 151 MET cc_start: 0.9017 (ttm) cc_final: 0.8254 (tpp) REVERT: C 166 TYR cc_start: 0.7996 (p90) cc_final: 0.7594 (p90) REVERT: C 192 PHE cc_start: 0.7763 (t80) cc_final: 0.7423 (t80) REVERT: C 215 THR cc_start: 0.8863 (t) cc_final: 0.8490 (m) REVERT: C 368 GLN cc_start: 0.9189 (tt0) cc_final: 0.8987 (tm-30) REVERT: C 977 MET cc_start: 0.8244 (mmp) cc_final: 0.7866 (mmm) REVERT: C 1015 GLN cc_start: 0.9287 (tp40) cc_final: 0.8522 (tp40) REVERT: C 1065 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8265 (tp-100) REVERT: C 1086 LEU cc_start: 0.7570 (tp) cc_final: 0.7210 (tp) REVERT: C 1122 ARG cc_start: 0.9061 (ttp-110) cc_final: 0.8797 (tmm-80) REVERT: D 169 ASP cc_start: 0.9111 (t0) cc_final: 0.8460 (t70) REVERT: D 194 LEU cc_start: 0.9237 (tp) cc_final: 0.9011 (tp) REVERT: D 237 LYS cc_start: 0.9135 (mmpt) cc_final: 0.8891 (mmmt) REVERT: D 297 HIS cc_start: 0.8818 (t70) cc_final: 0.8596 (m90) REVERT: D 366 PHE cc_start: 0.9162 (m-10) cc_final: 0.8949 (m-10) REVERT: D 370 ARG cc_start: 0.9039 (ptm160) cc_final: 0.8778 (ptm160) REVERT: D 393 TYR cc_start: 0.8783 (t80) cc_final: 0.8340 (t80) REVERT: D 410 ASN cc_start: 0.5902 (OUTLIER) cc_final: 0.5436 (t0) REVERT: D 569 ASP cc_start: 0.8379 (t0) cc_final: 0.8115 (t0) REVERT: D 916 PHE cc_start: 0.9002 (m-80) cc_final: 0.8708 (m-80) REVERT: D 960 GLN cc_start: 0.8170 (mp10) cc_final: 0.7780 (mt0) REVERT: D 1003 LYS cc_start: 0.8530 (tptt) cc_final: 0.8278 (tptt) REVERT: D 1132 TRP cc_start: 0.7225 (t-100) cc_final: 0.7003 (t-100) REVERT: D 1213 LEU cc_start: 0.9513 (tp) cc_final: 0.9295 (tp) REVERT: D 1297 ARG cc_start: 0.8888 (tmm-80) cc_final: 0.8614 (tmm-80) REVERT: D 1298 LEU cc_start: 0.9498 (pt) cc_final: 0.9253 (pt) REVERT: D 1325 GLN cc_start: 0.8788 (pp30) cc_final: 0.8570 (tm-30) REVERT: D 1328 LEU cc_start: 0.9355 (tt) cc_final: 0.8867 (tt) REVERT: D 1330 TYR cc_start: 0.9122 (p90) cc_final: 0.8753 (p90) REVERT: D 1393 LYS cc_start: 0.9088 (tmmt) cc_final: 0.8723 (tptt) REVERT: D 1397 LYS cc_start: 0.9622 (pptt) cc_final: 0.8472 (pttm) REVERT: D 1451 ASP cc_start: 0.3502 (OUTLIER) cc_final: 0.2471 (p0) outliers start: 20 outliers final: 6 residues processed: 734 average time/residue: 0.5781 time to fit residues: 679.8376 Evaluate side-chains 519 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 507 time to evaluate : 4.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 452 optimal weight: 6.9990 chunk 406 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 420 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 312 optimal weight: 20.0000 chunk 486 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A1009 ASN A1062 HIS ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** A1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 217 HIS ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 ASN B1013 GLN ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1302 GLN ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN C1009 ASN C1062 HIS C1118 HIS C1136 GLN ** C1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 ASN D1013 GLN ** D1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1302 GLN ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 43574 Z= 0.332 Angle : 0.940 13.735 59204 Z= 0.472 Chirality : 0.053 0.399 6900 Planarity : 0.006 0.075 7554 Dihedral : 10.946 70.761 6812 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.29 % Favored : 85.52 % Rotamer: Outliers : 0.30 % Allowed : 8.72 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.08 % 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: -4.73 (0.09), residues: 5360 helix: -1.97 (0.15), residues: 802 sheet: -2.78 (0.11), residues: 1512 loop : -3.82 (0.09), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D1183 HIS 0.012 0.002 HIS B1020 PHE 0.033 0.002 PHE D 808 TYR 0.036 0.002 TYR B1418 ARG 0.006 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 621 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9566 (mp) cc_final: 0.9317 (mp) REVERT: A 55 ASN cc_start: 0.6802 (p0) cc_final: 0.5061 (t0) REVERT: A 121 MET cc_start: 0.9511 (pmm) cc_final: 0.9279 (pmm) REVERT: A 151 MET cc_start: 0.9039 (ttm) cc_final: 0.8798 (ttm) REVERT: A 166 TYR cc_start: 0.8207 (p90) cc_final: 0.7888 (p90) REVERT: A 192 PHE cc_start: 0.7840 (t80) cc_final: 0.7487 (t80) REVERT: A 464 MET cc_start: 0.7978 (mtt) cc_final: 0.7507 (mtt) REVERT: A 666 MET cc_start: 0.8824 (tpp) cc_final: 0.8594 (tpp) REVERT: A 931 LEU cc_start: 0.9448 (tt) cc_final: 0.8935 (mp) REVERT: A 968 MET cc_start: 0.2493 (mmt) cc_final: 0.2129 (mmt) REVERT: A 1003 LYS cc_start: 0.8676 (tptp) cc_final: 0.8302 (tptp) REVERT: A 1015 GLN cc_start: 0.9235 (tp40) cc_final: 0.8874 (tp40) REVERT: A 1065 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8257 (tp-100) REVERT: A 1122 ARG cc_start: 0.9025 (ttp-110) cc_final: 0.8697 (tmm-80) REVERT: A 1254 THR cc_start: 0.9253 (m) cc_final: 0.8906 (m) REVERT: B 169 ASP cc_start: 0.8884 (t0) cc_final: 0.8584 (t0) REVERT: B 194 LEU cc_start: 0.9087 (tp) cc_final: 0.8859 (tp) REVERT: B 229 PHE cc_start: 0.9214 (p90) cc_final: 0.8971 (p90) REVERT: B 300 PHE cc_start: 0.8743 (t80) cc_final: 0.8501 (t80) REVERT: B 370 ARG cc_start: 0.9131 (ptm160) cc_final: 0.8890 (ptm160) REVERT: B 393 TYR cc_start: 0.8828 (t80) cc_final: 0.8620 (m-80) REVERT: B 546 LEU cc_start: 0.8813 (tp) cc_final: 0.8607 (tp) REVERT: B 569 ASP cc_start: 0.8611 (t0) cc_final: 0.8349 (t0) REVERT: B 571 SER cc_start: 0.9142 (t) cc_final: 0.8620 (p) REVERT: B 817 TYR cc_start: 0.8382 (m-10) cc_final: 0.8084 (m-80) REVERT: B 916 PHE cc_start: 0.9082 (m-80) cc_final: 0.8774 (m-80) REVERT: B 933 LEU cc_start: 0.9282 (mp) cc_final: 0.9065 (mp) REVERT: B 1073 ARG cc_start: 0.7582 (mtm110) cc_final: 0.7252 (mtm110) REVERT: B 1109 LEU cc_start: 0.9568 (mt) cc_final: 0.9299 (mt) REVERT: B 1291 GLN cc_start: 0.9238 (pm20) cc_final: 0.8969 (pp30) REVERT: B 1293 ASP cc_start: 0.9609 (m-30) cc_final: 0.8897 (m-30) REVERT: B 1299 LEU cc_start: 0.9334 (mm) cc_final: 0.9047 (mt) REVERT: B 1328 LEU cc_start: 0.9274 (tt) cc_final: 0.8741 (tt) REVERT: B 1330 TYR cc_start: 0.9375 (p90) cc_final: 0.8890 (p90) REVERT: B 1431 PHE cc_start: 0.8732 (p90) cc_final: 0.8485 (p90) REVERT: C 34 LEU cc_start: 0.9568 (mp) cc_final: 0.9318 (mp) REVERT: C 55 ASN cc_start: 0.6798 (p0) cc_final: 0.5059 (t0) REVERT: C 121 MET cc_start: 0.9510 (pmm) cc_final: 0.9278 (pmm) REVERT: C 151 MET cc_start: 0.9034 (ttm) cc_final: 0.8795 (ttm) REVERT: C 166 TYR cc_start: 0.8214 (p90) cc_final: 0.7887 (p90) REVERT: C 192 PHE cc_start: 0.7841 (t80) cc_final: 0.7489 (t80) REVERT: C 464 MET cc_start: 0.7978 (mtt) cc_final: 0.7505 (mtt) REVERT: C 666 MET cc_start: 0.8824 (tpp) cc_final: 0.8595 (tpp) REVERT: C 931 LEU cc_start: 0.9450 (tt) cc_final: 0.8938 (mp) REVERT: C 968 MET cc_start: 0.2434 (mmt) cc_final: 0.2146 (mmt) REVERT: C 1003 LYS cc_start: 0.8678 (tptp) cc_final: 0.8304 (tptp) REVERT: C 1015 GLN cc_start: 0.9195 (tp40) cc_final: 0.8857 (tp40) REVERT: C 1065 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8260 (tp-100) REVERT: C 1122 ARG cc_start: 0.9025 (ttp-110) cc_final: 0.8708 (tmm-80) REVERT: C 1254 THR cc_start: 0.9253 (m) cc_final: 0.8905 (m) REVERT: D 169 ASP cc_start: 0.8886 (t0) cc_final: 0.8587 (t0) REVERT: D 194 LEU cc_start: 0.9087 (tp) cc_final: 0.8860 (tp) REVERT: D 229 PHE cc_start: 0.9215 (p90) cc_final: 0.8972 (p90) REVERT: D 300 PHE cc_start: 0.8745 (t80) cc_final: 0.8503 (t80) REVERT: D 370 ARG cc_start: 0.9131 (ptm160) cc_final: 0.8890 (ptm160) REVERT: D 393 TYR cc_start: 0.8829 (t80) cc_final: 0.8621 (m-80) REVERT: D 546 LEU cc_start: 0.8811 (tp) cc_final: 0.8605 (tp) REVERT: D 569 ASP cc_start: 0.8615 (t0) cc_final: 0.8353 (t0) REVERT: D 571 SER cc_start: 0.9145 (t) cc_final: 0.8623 (p) REVERT: D 817 TYR cc_start: 0.8379 (m-10) cc_final: 0.8082 (m-80) REVERT: D 916 PHE cc_start: 0.9085 (m-80) cc_final: 0.8777 (m-80) REVERT: D 933 LEU cc_start: 0.9279 (mp) cc_final: 0.9064 (mp) REVERT: D 1073 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7259 (mtm110) REVERT: D 1109 LEU cc_start: 0.9566 (mt) cc_final: 0.9297 (mt) REVERT: D 1291 GLN cc_start: 0.9236 (pm20) cc_final: 0.8971 (pp30) REVERT: D 1293 ASP cc_start: 0.9609 (m-30) cc_final: 0.8894 (m-30) REVERT: D 1299 LEU cc_start: 0.9333 (mm) cc_final: 0.9044 (mt) REVERT: D 1328 LEU cc_start: 0.9279 (tt) cc_final: 0.8744 (tt) REVERT: D 1330 TYR cc_start: 0.9377 (p90) cc_final: 0.8891 (p90) REVERT: D 1431 PHE cc_start: 0.8707 (p90) cc_final: 0.8464 (p90) outliers start: 14 outliers final: 3 residues processed: 633 average time/residue: 0.5434 time to fit residues: 562.8521 Evaluate side-chains 473 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 5.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 405 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 487 optimal weight: 2.9990 chunk 526 optimal weight: 9.9990 chunk 434 optimal weight: 7.9990 chunk 483 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 391 optimal weight: 0.6980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 HIS ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A1062 HIS ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN B1195 HIS ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 846 HIS ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN C1062 HIS ** C1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN D 302 GLN D 566 ASN ** D 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 43574 Z= 0.261 Angle : 0.840 12.938 59204 Z= 0.422 Chirality : 0.051 0.449 6900 Planarity : 0.006 0.066 7554 Dihedral : 9.288 59.488 6812 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.99 % Favored : 85.78 % Rotamer: Outliers : 0.19 % Allowed : 6.95 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.33 (0.10), residues: 5360 helix: -1.46 (0.16), residues: 802 sheet: -2.48 (0.12), residues: 1522 loop : -3.64 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B1183 HIS 0.015 0.001 HIS A1020 PHE 0.049 0.002 PHE D1049 TYR 0.033 0.002 TYR D1418 ARG 0.004 0.001 ARG A1081 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 619 time to evaluate : 4.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6690 (p0) cc_final: 0.4959 (t0) REVERT: A 121 MET cc_start: 0.9512 (pmm) cc_final: 0.9161 (pmm) REVERT: A 151 MET cc_start: 0.9052 (ttm) cc_final: 0.8819 (ttm) REVERT: A 166 TYR cc_start: 0.8084 (p90) cc_final: 0.7843 (p90) REVERT: A 192 PHE cc_start: 0.7763 (t80) cc_final: 0.7428 (t80) REVERT: A 373 ASP cc_start: 0.9533 (p0) cc_final: 0.9028 (m-30) REVERT: A 464 MET cc_start: 0.8071 (mtt) cc_final: 0.7518 (mtt) REVERT: A 931 LEU cc_start: 0.9351 (tt) cc_final: 0.8803 (mp) REVERT: A 968 MET cc_start: 0.3060 (mmt) cc_final: 0.2771 (mmt) REVERT: A 1003 LYS cc_start: 0.8552 (tptp) cc_final: 0.8286 (tppt) REVERT: A 1015 GLN cc_start: 0.9224 (tp40) cc_final: 0.8919 (tp40) REVERT: A 1065 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8264 (tp-100) REVERT: A 1111 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7988 (mp0) REVERT: A 1122 ARG cc_start: 0.8974 (ttp-110) cc_final: 0.8557 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6589 (tt) cc_final: 0.6163 (tt) REVERT: B 145 LYS cc_start: 0.7382 (ptpt) cc_final: 0.6250 (ptpt) REVERT: B 151 MET cc_start: 0.9147 (mtp) cc_final: 0.8856 (ttm) REVERT: B 169 ASP cc_start: 0.8832 (t0) cc_final: 0.8498 (t70) REVERT: B 370 ARG cc_start: 0.9103 (ptm160) cc_final: 0.8782 (ptm160) REVERT: B 495 PHE cc_start: 0.7253 (m-80) cc_final: 0.6695 (m-80) REVERT: B 552 ILE cc_start: 0.8603 (mm) cc_final: 0.8374 (mm) REVERT: B 571 SER cc_start: 0.9123 (t) cc_final: 0.8877 (p) REVERT: B 597 LEU cc_start: 0.9221 (mt) cc_final: 0.8975 (mt) REVERT: B 741 TRP cc_start: 0.7842 (t60) cc_final: 0.7593 (t-100) REVERT: B 743 LEU cc_start: 0.9123 (mp) cc_final: 0.8729 (tp) REVERT: B 817 TYR cc_start: 0.8214 (m-10) cc_final: 0.7994 (m-80) REVERT: B 1109 LEU cc_start: 0.9599 (mt) cc_final: 0.9319 (mt) REVERT: B 1132 TRP cc_start: 0.7045 (t-100) cc_final: 0.6492 (t-100) REVERT: B 1168 LYS cc_start: 0.9500 (tptt) cc_final: 0.9177 (tptt) REVERT: B 1291 GLN cc_start: 0.9310 (pm20) cc_final: 0.9042 (pp30) REVERT: B 1293 ASP cc_start: 0.9593 (m-30) cc_final: 0.8783 (m-30) REVERT: B 1299 LEU cc_start: 0.9387 (mm) cc_final: 0.9112 (mt) REVERT: B 1323 TYR cc_start: 0.6238 (t80) cc_final: 0.5669 (t80) REVERT: B 1431 PHE cc_start: 0.8734 (p90) cc_final: 0.8506 (p90) REVERT: C 55 ASN cc_start: 0.6689 (p0) cc_final: 0.4960 (t0) REVERT: C 121 MET cc_start: 0.9512 (pmm) cc_final: 0.9159 (pmm) REVERT: C 151 MET cc_start: 0.9046 (ttm) cc_final: 0.8815 (ttm) REVERT: C 166 TYR cc_start: 0.8089 (p90) cc_final: 0.7847 (p90) REVERT: C 192 PHE cc_start: 0.7765 (t80) cc_final: 0.7431 (t80) REVERT: C 373 ASP cc_start: 0.9530 (p0) cc_final: 0.9031 (m-30) REVERT: C 464 MET cc_start: 0.8072 (mtt) cc_final: 0.7519 (mtt) REVERT: C 931 LEU cc_start: 0.9354 (tt) cc_final: 0.8809 (mp) REVERT: C 968 MET cc_start: 0.3044 (mmt) cc_final: 0.2762 (mmt) REVERT: C 1003 LYS cc_start: 0.8552 (tptp) cc_final: 0.8288 (tppt) REVERT: C 1015 GLN cc_start: 0.9230 (tp40) cc_final: 0.8930 (tp40) REVERT: C 1065 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8265 (tp-100) REVERT: C 1111 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7985 (mp0) REVERT: C 1122 ARG cc_start: 0.8984 (ttp-110) cc_final: 0.8584 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6592 (tt) cc_final: 0.6170 (tt) REVERT: D 145 LYS cc_start: 0.7388 (ptpt) cc_final: 0.6256 (ptpt) REVERT: D 151 MET cc_start: 0.9149 (mtp) cc_final: 0.8858 (ttm) REVERT: D 169 ASP cc_start: 0.8835 (t0) cc_final: 0.8503 (t70) REVERT: D 370 ARG cc_start: 0.9103 (ptm160) cc_final: 0.8784 (ptm160) REVERT: D 495 PHE cc_start: 0.7259 (m-80) cc_final: 0.6700 (m-80) REVERT: D 552 ILE cc_start: 0.8610 (mm) cc_final: 0.8381 (mm) REVERT: D 571 SER cc_start: 0.9126 (t) cc_final: 0.8882 (p) REVERT: D 597 LEU cc_start: 0.9227 (mt) cc_final: 0.8981 (mt) REVERT: D 741 TRP cc_start: 0.7842 (t60) cc_final: 0.7595 (t-100) REVERT: D 743 LEU cc_start: 0.9126 (mp) cc_final: 0.8730 (tp) REVERT: D 817 TYR cc_start: 0.8211 (m-10) cc_final: 0.7991 (m-80) REVERT: D 1109 LEU cc_start: 0.9596 (mt) cc_final: 0.9317 (mt) REVERT: D 1291 GLN cc_start: 0.9306 (pm20) cc_final: 0.9043 (pp30) REVERT: D 1293 ASP cc_start: 0.9594 (m-30) cc_final: 0.8782 (m-30) REVERT: D 1299 LEU cc_start: 0.9388 (mm) cc_final: 0.9113 (mt) REVERT: D 1431 PHE cc_start: 0.8717 (p90) cc_final: 0.8413 (p90) outliers start: 9 outliers final: 1 residues processed: 625 average time/residue: 0.5292 time to fit residues: 542.4516 Evaluate side-chains 479 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 478 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 20.0000 chunk 366 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 489 optimal weight: 4.9990 chunk 518 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 463 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 HIS ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A1062 HIS ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 ASN A1302 GLN B 460 HIS ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 HIS ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN C1062 HIS C1159 ASN C1302 GLN D 460 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43574 Z= 0.288 Angle : 0.841 11.073 59204 Z= 0.427 Chirality : 0.051 0.451 6900 Planarity : 0.006 0.084 7554 Dihedral : 8.812 58.760 6812 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 32.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.34 % Favored : 84.51 % Rotamer: Outliers : 0.15 % Allowed : 6.19 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.17 (0.10), residues: 5360 helix: -1.35 (0.16), residues: 804 sheet: -2.35 (0.12), residues: 1534 loop : -3.54 (0.09), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D1132 HIS 0.010 0.002 HIS B1414 PHE 0.035 0.002 PHE D1049 TYR 0.037 0.002 TYR B1418 ARG 0.004 0.001 ARG D 732 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 588 time to evaluate : 4.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9438 (tmm) cc_final: 0.9072 (tmm) REVERT: A 34 LEU cc_start: 0.9498 (mt) cc_final: 0.9271 (mt) REVERT: A 55 ASN cc_start: 0.6836 (p0) cc_final: 0.5151 (t0) REVERT: A 166 TYR cc_start: 0.8284 (p90) cc_final: 0.8045 (p90) REVERT: A 192 PHE cc_start: 0.7854 (t80) cc_final: 0.7458 (t80) REVERT: A 373 ASP cc_start: 0.9415 (p0) cc_final: 0.9105 (m-30) REVERT: A 464 MET cc_start: 0.8172 (mtt) cc_final: 0.7657 (mtt) REVERT: A 598 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7671 (ttp-170) REVERT: A 666 MET cc_start: 0.8979 (tpp) cc_final: 0.8729 (tpp) REVERT: A 931 LEU cc_start: 0.9402 (tt) cc_final: 0.8868 (mp) REVERT: A 968 MET cc_start: 0.2918 (mmt) cc_final: 0.2610 (mmt) REVERT: A 1003 LYS cc_start: 0.8627 (tptp) cc_final: 0.8364 (tppt) REVERT: A 1015 GLN cc_start: 0.9227 (tp40) cc_final: 0.8736 (tp40) REVERT: A 1065 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8275 (tp-100) REVERT: A 1122 ARG cc_start: 0.8974 (ttp-110) cc_final: 0.8566 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6858 (tt) cc_final: 0.6537 (tt) REVERT: B 151 MET cc_start: 0.9270 (mtp) cc_final: 0.8904 (ttm) REVERT: B 169 ASP cc_start: 0.8393 (t0) cc_final: 0.7951 (t70) REVERT: B 194 LEU cc_start: 0.9197 (tp) cc_final: 0.8944 (tp) REVERT: B 370 ARG cc_start: 0.9085 (ptm160) cc_final: 0.8753 (ptm160) REVERT: B 385 PHE cc_start: 0.8437 (m-80) cc_final: 0.8228 (m-80) REVERT: B 393 TYR cc_start: 0.7839 (m-80) cc_final: 0.7627 (m-80) REVERT: B 495 PHE cc_start: 0.7396 (m-80) cc_final: 0.6958 (m-80) REVERT: B 552 ILE cc_start: 0.8926 (mm) cc_final: 0.8622 (mm) REVERT: B 570 LEU cc_start: 0.8372 (pp) cc_final: 0.8152 (pp) REVERT: B 571 SER cc_start: 0.9155 (t) cc_final: 0.8854 (p) REVERT: B 597 LEU cc_start: 0.9259 (mt) cc_final: 0.9026 (mt) REVERT: B 743 LEU cc_start: 0.9226 (mp) cc_final: 0.8735 (tt) REVERT: B 817 TYR cc_start: 0.8183 (m-10) cc_final: 0.7891 (m-80) REVERT: B 841 LYS cc_start: 0.9531 (tptm) cc_final: 0.9302 (tmtt) REVERT: B 1007 TYR cc_start: 0.9361 (m-80) cc_final: 0.9146 (m-80) REVERT: B 1020 HIS cc_start: 0.8533 (m90) cc_final: 0.8040 (m170) REVERT: B 1109 LEU cc_start: 0.9649 (mt) cc_final: 0.9383 (mt) REVERT: B 1291 GLN cc_start: 0.9324 (pm20) cc_final: 0.9077 (pp30) REVERT: B 1293 ASP cc_start: 0.9596 (m-30) cc_final: 0.8815 (m-30) REVERT: B 1299 LEU cc_start: 0.9379 (mm) cc_final: 0.9104 (mt) REVERT: B 1353 ASP cc_start: 0.7966 (m-30) cc_final: 0.7485 (p0) REVERT: C 32 MET cc_start: 0.9437 (tmm) cc_final: 0.9070 (tmm) REVERT: C 34 LEU cc_start: 0.9499 (mt) cc_final: 0.9272 (mt) REVERT: C 55 ASN cc_start: 0.6836 (p0) cc_final: 0.5151 (t0) REVERT: C 166 TYR cc_start: 0.8288 (p90) cc_final: 0.8047 (p90) REVERT: C 192 PHE cc_start: 0.7853 (t80) cc_final: 0.7458 (t80) REVERT: C 373 ASP cc_start: 0.9417 (p0) cc_final: 0.9105 (m-30) REVERT: C 464 MET cc_start: 0.8170 (mtt) cc_final: 0.7658 (mtt) REVERT: C 598 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7672 (ttp-170) REVERT: C 666 MET cc_start: 0.8955 (tpp) cc_final: 0.8714 (tpp) REVERT: C 931 LEU cc_start: 0.9405 (tt) cc_final: 0.8874 (mp) REVERT: C 968 MET cc_start: 0.2914 (mmt) cc_final: 0.2603 (mmt) REVERT: C 1003 LYS cc_start: 0.8628 (tptp) cc_final: 0.8367 (tppt) REVERT: C 1015 GLN cc_start: 0.9231 (tp40) cc_final: 0.8739 (tp40) REVERT: C 1065 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8274 (tp-100) REVERT: C 1122 ARG cc_start: 0.8981 (ttp-110) cc_final: 0.8558 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6862 (tt) cc_final: 0.6541 (tt) REVERT: D 151 MET cc_start: 0.9269 (mtp) cc_final: 0.8899 (ttm) REVERT: D 169 ASP cc_start: 0.8391 (t0) cc_final: 0.7948 (t70) REVERT: D 194 LEU cc_start: 0.9195 (tp) cc_final: 0.8943 (tp) REVERT: D 370 ARG cc_start: 0.9086 (ptm160) cc_final: 0.8755 (ptm160) REVERT: D 385 PHE cc_start: 0.8438 (m-80) cc_final: 0.8231 (m-80) REVERT: D 393 TYR cc_start: 0.7841 (m-80) cc_final: 0.7628 (m-80) REVERT: D 495 PHE cc_start: 0.7400 (m-80) cc_final: 0.6961 (m-80) REVERT: D 520 MET cc_start: 0.5854 (tpp) cc_final: 0.5633 (tpp) REVERT: D 552 ILE cc_start: 0.8929 (mm) cc_final: 0.8627 (mm) REVERT: D 570 LEU cc_start: 0.8382 (pp) cc_final: 0.8162 (pp) REVERT: D 571 SER cc_start: 0.9160 (t) cc_final: 0.8862 (p) REVERT: D 597 LEU cc_start: 0.9265 (mt) cc_final: 0.9032 (mt) REVERT: D 743 LEU cc_start: 0.9229 (mp) cc_final: 0.8737 (tt) REVERT: D 817 TYR cc_start: 0.8180 (m-10) cc_final: 0.7888 (m-80) REVERT: D 841 LYS cc_start: 0.9530 (tptm) cc_final: 0.9301 (tmtt) REVERT: D 1007 TYR cc_start: 0.9350 (m-80) cc_final: 0.9144 (m-80) REVERT: D 1020 HIS cc_start: 0.8503 (m90) cc_final: 0.8209 (m-70) REVERT: D 1109 LEU cc_start: 0.9652 (mt) cc_final: 0.9398 (mt) REVERT: D 1150 LEU cc_start: 0.9218 (mt) cc_final: 0.8997 (mt) REVERT: D 1173 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9034 (mt-10) REVERT: D 1291 GLN cc_start: 0.9325 (pm20) cc_final: 0.9079 (pp30) REVERT: D 1293 ASP cc_start: 0.9597 (m-30) cc_final: 0.8811 (m-30) REVERT: D 1299 LEU cc_start: 0.9377 (mm) cc_final: 0.9103 (mt) REVERT: D 1353 ASP cc_start: 0.7965 (m-30) cc_final: 0.7485 (p0) outliers start: 7 outliers final: 3 residues processed: 592 average time/residue: 0.5551 time to fit residues: 536.4157 Evaluate side-chains 466 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 463 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 213 optimal weight: 0.0970 chunk 442 optimal weight: 7.9990 chunk 358 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 chunk 465 optimal weight: 2.9990 chunk 130 optimal weight: 40.0000 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A1062 HIS A1077 ASN ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1435 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS C 576 GLN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN ** C 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS C1077 ASN ** C1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 43574 Z= 0.252 Angle : 0.809 10.371 59204 Z= 0.408 Chirality : 0.050 0.438 6900 Planarity : 0.006 0.064 7554 Dihedral : 8.508 59.926 6812 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 31.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.85 % Favored : 85.04 % Rotamer: Outliers : 0.09 % Allowed : 3.89 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.99 (0.10), residues: 5360 helix: -1.17 (0.16), residues: 818 sheet: -2.21 (0.13), residues: 1464 loop : -3.44 (0.09), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 741 HIS 0.018 0.001 HIS B1020 PHE 0.036 0.002 PHE D1049 TYR 0.033 0.002 TYR D1418 ARG 0.009 0.001 ARG B 732 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 595 time to evaluate : 4.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9429 (tmm) cc_final: 0.9089 (tmm) REVERT: A 55 ASN cc_start: 0.6914 (p0) cc_final: 0.5318 (t0) REVERT: A 121 MET cc_start: 0.9458 (pmm) cc_final: 0.9189 (pmm) REVERT: A 151 MET cc_start: 0.9016 (ttm) cc_final: 0.8198 (tpp) REVERT: A 166 TYR cc_start: 0.8270 (p90) cc_final: 0.8061 (p90) REVERT: A 192 PHE cc_start: 0.7915 (t80) cc_final: 0.7478 (t80) REVERT: A 373 ASP cc_start: 0.9481 (p0) cc_final: 0.9110 (m-30) REVERT: A 638 ASP cc_start: 0.9189 (t70) cc_final: 0.8922 (t0) REVERT: A 931 LEU cc_start: 0.9362 (tt) cc_final: 0.8828 (mp) REVERT: A 968 MET cc_start: 0.2792 (mmt) cc_final: 0.2510 (mmt) REVERT: A 1003 LYS cc_start: 0.8645 (tptp) cc_final: 0.8366 (tppt) REVERT: A 1208 MET cc_start: 0.8984 (ppp) cc_final: 0.8749 (ppp) REVERT: A 1211 TYR cc_start: 0.8554 (m-80) cc_final: 0.8229 (m-80) REVERT: A 1214 LEU cc_start: 0.6943 (tt) cc_final: 0.6627 (tt) REVERT: B 151 MET cc_start: 0.9287 (mtp) cc_final: 0.8903 (ttm) REVERT: B 169 ASP cc_start: 0.8270 (t0) cc_final: 0.7839 (t70) REVERT: B 194 LEU cc_start: 0.9185 (tp) cc_final: 0.8976 (tp) REVERT: B 370 ARG cc_start: 0.9062 (ptm160) cc_final: 0.8712 (ptm160) REVERT: B 385 PHE cc_start: 0.8439 (m-80) cc_final: 0.8218 (m-80) REVERT: B 495 PHE cc_start: 0.7608 (m-80) cc_final: 0.7292 (m-80) REVERT: B 552 ILE cc_start: 0.8837 (mm) cc_final: 0.8608 (mm) REVERT: B 571 SER cc_start: 0.9198 (t) cc_final: 0.8906 (p) REVERT: B 597 LEU cc_start: 0.9243 (mt) cc_final: 0.8984 (mt) REVERT: B 743 LEU cc_start: 0.9193 (mp) cc_final: 0.8706 (tt) REVERT: B 841 LYS cc_start: 0.9550 (tptm) cc_final: 0.9309 (tmtt) REVERT: B 1109 LEU cc_start: 0.9628 (mt) cc_final: 0.9362 (mt) REVERT: B 1145 TYR cc_start: 0.8667 (m-10) cc_final: 0.7788 (m-10) REVERT: B 1150 LEU cc_start: 0.9233 (mt) cc_final: 0.8859 (mm) REVERT: B 1208 MET cc_start: 0.9404 (ppp) cc_final: 0.9201 (ppp) REVERT: B 1209 THR cc_start: 0.8898 (t) cc_final: 0.8614 (t) REVERT: B 1248 PHE cc_start: 0.7829 (t80) cc_final: 0.7179 (t80) REVERT: B 1291 GLN cc_start: 0.9318 (pm20) cc_final: 0.9109 (pp30) REVERT: B 1293 ASP cc_start: 0.9613 (m-30) cc_final: 0.8857 (m-30) REVERT: B 1299 LEU cc_start: 0.9381 (mm) cc_final: 0.9110 (mt) REVERT: C 32 MET cc_start: 0.9430 (tmm) cc_final: 0.9088 (tmm) REVERT: C 55 ASN cc_start: 0.6917 (p0) cc_final: 0.5316 (t0) REVERT: C 121 MET cc_start: 0.9457 (pmm) cc_final: 0.9193 (pmm) REVERT: C 151 MET cc_start: 0.9013 (ttm) cc_final: 0.8195 (tpp) REVERT: C 166 TYR cc_start: 0.8274 (p90) cc_final: 0.8063 (p90) REVERT: C 192 PHE cc_start: 0.7914 (t80) cc_final: 0.7480 (t80) REVERT: C 373 ASP cc_start: 0.9480 (p0) cc_final: 0.9110 (m-30) REVERT: C 576 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.4796 (pp30) REVERT: C 638 ASP cc_start: 0.9188 (t70) cc_final: 0.8920 (t0) REVERT: C 931 LEU cc_start: 0.9366 (tt) cc_final: 0.8835 (mp) REVERT: C 968 MET cc_start: 0.2781 (mmt) cc_final: 0.2501 (mmt) REVERT: C 1003 LYS cc_start: 0.8631 (tptp) cc_final: 0.8348 (tppt) REVERT: C 1208 MET cc_start: 0.8981 (ppp) cc_final: 0.8746 (ppp) REVERT: C 1211 TYR cc_start: 0.8557 (m-80) cc_final: 0.8230 (m-80) REVERT: C 1214 LEU cc_start: 0.6947 (tt) cc_final: 0.6630 (tt) REVERT: D 151 MET cc_start: 0.9288 (mtp) cc_final: 0.8902 (ttm) REVERT: D 169 ASP cc_start: 0.8288 (t0) cc_final: 0.7844 (t70) REVERT: D 194 LEU cc_start: 0.9181 (tp) cc_final: 0.8973 (tp) REVERT: D 370 ARG cc_start: 0.9063 (ptm160) cc_final: 0.8717 (ptm160) REVERT: D 385 PHE cc_start: 0.8438 (m-80) cc_final: 0.8216 (m-80) REVERT: D 495 PHE cc_start: 0.7614 (m-80) cc_final: 0.7298 (m-80) REVERT: D 520 MET cc_start: 0.5973 (tpp) cc_final: 0.5747 (tpp) REVERT: D 552 ILE cc_start: 0.8845 (mm) cc_final: 0.8621 (mm) REVERT: D 558 TYR cc_start: 0.8835 (m-80) cc_final: 0.8633 (m-80) REVERT: D 571 SER cc_start: 0.9202 (t) cc_final: 0.8911 (p) REVERT: D 597 LEU cc_start: 0.9247 (mt) cc_final: 0.8987 (mt) REVERT: D 743 LEU cc_start: 0.9195 (mp) cc_final: 0.8704 (tt) REVERT: D 841 LYS cc_start: 0.9550 (tptm) cc_final: 0.9309 (tmtt) REVERT: D 1109 LEU cc_start: 0.9653 (mt) cc_final: 0.9387 (mt) REVERT: D 1195 HIS cc_start: 0.6966 (t70) cc_final: 0.6349 (t-170) REVERT: D 1208 MET cc_start: 0.9400 (ppp) cc_final: 0.9194 (ppp) REVERT: D 1209 THR cc_start: 0.8903 (t) cc_final: 0.8621 (t) REVERT: D 1248 PHE cc_start: 0.7836 (t80) cc_final: 0.7191 (t80) REVERT: D 1291 GLN cc_start: 0.9317 (pm20) cc_final: 0.9109 (pp30) REVERT: D 1293 ASP cc_start: 0.9613 (m-30) cc_final: 0.8854 (m-30) REVERT: D 1299 LEU cc_start: 0.9374 (mm) cc_final: 0.9106 (mt) outliers start: 4 outliers final: 1 residues processed: 598 average time/residue: 0.5306 time to fit residues: 526.9923 Evaluate side-chains 472 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 470 time to evaluate : 4.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 20.0000 chunk 466 optimal weight: 0.0070 chunk 102 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 518 optimal weight: 1.9990 chunk 430 optimal weight: 0.8980 chunk 240 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 171 optimal weight: 0.3980 chunk 272 optimal weight: 10.0000 overall best weight: 2.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN ** C 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN ** C 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS C1187 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1414 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43574 Z= 0.209 Angle : 0.785 11.863 59204 Z= 0.390 Chirality : 0.050 0.424 6900 Planarity : 0.005 0.065 7554 Dihedral : 8.322 59.683 6812 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 26.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.90 % Favored : 85.99 % Rotamer: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.82 (0.10), residues: 5360 helix: -0.95 (0.17), residues: 804 sheet: -2.07 (0.13), residues: 1502 loop : -3.37 (0.10), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D1132 HIS 0.019 0.001 HIS A1020 PHE 0.020 0.002 PHE B 458 TYR 0.032 0.002 TYR D1418 ARG 0.007 0.000 ARG D1031 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 608 time to evaluate : 4.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9496 (mt) cc_final: 0.9242 (mp) REVERT: A 55 ASN cc_start: 0.7063 (p0) cc_final: 0.5450 (t0) REVERT: A 121 MET cc_start: 0.9441 (pmm) cc_final: 0.9189 (pmm) REVERT: A 151 MET cc_start: 0.9004 (ttm) cc_final: 0.8154 (tpp) REVERT: A 192 PHE cc_start: 0.7830 (t80) cc_final: 0.7550 (t80) REVERT: A 250 VAL cc_start: 0.9311 (m) cc_final: 0.9022 (p) REVERT: A 263 HIS cc_start: 0.9205 (m-70) cc_final: 0.8991 (t-90) REVERT: A 373 ASP cc_start: 0.9478 (p0) cc_final: 0.9082 (m-30) REVERT: A 464 MET cc_start: 0.8270 (mtt) cc_final: 0.7810 (mtt) REVERT: A 576 GLN cc_start: 0.5275 (OUTLIER) cc_final: 0.5048 (pp30) REVERT: A 638 ASP cc_start: 0.9225 (t70) cc_final: 0.8959 (t70) REVERT: A 968 MET cc_start: 0.2626 (mmt) cc_final: 0.2391 (mmt) REVERT: A 1003 LYS cc_start: 0.8631 (tptp) cc_final: 0.8368 (tppt) REVERT: A 1015 GLN cc_start: 0.9215 (tp40) cc_final: 0.8432 (tp40) REVERT: A 1047 LYS cc_start: 0.8378 (pttt) cc_final: 0.8112 (ptpp) REVERT: A 1214 LEU cc_start: 0.6612 (tt) cc_final: 0.6210 (pp) REVERT: B 151 MET cc_start: 0.9247 (mtp) cc_final: 0.8971 (ttt) REVERT: B 370 ARG cc_start: 0.9051 (ptm160) cc_final: 0.8700 (ptm160) REVERT: B 385 PHE cc_start: 0.8426 (m-80) cc_final: 0.8194 (m-80) REVERT: B 432 TYR cc_start: 0.9148 (t80) cc_final: 0.8765 (t80) REVERT: B 495 PHE cc_start: 0.7536 (m-80) cc_final: 0.7296 (m-80) REVERT: B 571 SER cc_start: 0.9049 (t) cc_final: 0.8812 (p) REVERT: B 597 LEU cc_start: 0.9181 (mt) cc_final: 0.8920 (mt) REVERT: B 743 LEU cc_start: 0.9134 (mp) cc_final: 0.8760 (tt) REVERT: B 841 LYS cc_start: 0.9547 (tptm) cc_final: 0.9323 (tmtt) REVERT: B 916 PHE cc_start: 0.9027 (m-10) cc_final: 0.8719 (m-10) REVERT: B 933 LEU cc_start: 0.9388 (mp) cc_final: 0.9187 (mp) REVERT: B 1092 LYS cc_start: 0.9325 (mmtm) cc_final: 0.8872 (tmtt) REVERT: B 1109 LEU cc_start: 0.9585 (mt) cc_final: 0.9290 (mt) REVERT: B 1145 TYR cc_start: 0.8430 (m-10) cc_final: 0.8092 (m-10) REVERT: B 1150 LEU cc_start: 0.9343 (mt) cc_final: 0.8569 (mm) REVERT: B 1248 PHE cc_start: 0.7908 (t80) cc_final: 0.7229 (t80) REVERT: B 1291 GLN cc_start: 0.9317 (pm20) cc_final: 0.9110 (pp30) REVERT: B 1293 ASP cc_start: 0.9608 (m-30) cc_final: 0.8826 (m-30) REVERT: B 1389 PHE cc_start: 0.8842 (m-80) cc_final: 0.8269 (m-80) REVERT: B 1431 PHE cc_start: 0.8810 (p90) cc_final: 0.8456 (p90) REVERT: C 34 LEU cc_start: 0.9498 (mt) cc_final: 0.9238 (mp) REVERT: C 55 ASN cc_start: 0.7063 (p0) cc_final: 0.5454 (t0) REVERT: C 121 MET cc_start: 0.9441 (pmm) cc_final: 0.9186 (pmm) REVERT: C 151 MET cc_start: 0.9000 (ttm) cc_final: 0.8150 (tpp) REVERT: C 192 PHE cc_start: 0.7827 (t80) cc_final: 0.7550 (t80) REVERT: C 250 VAL cc_start: 0.9312 (m) cc_final: 0.9023 (p) REVERT: C 263 HIS cc_start: 0.9206 (m-70) cc_final: 0.8991 (t-90) REVERT: C 373 ASP cc_start: 0.9478 (p0) cc_final: 0.9083 (m-30) REVERT: C 464 MET cc_start: 0.8240 (mtt) cc_final: 0.7794 (mtt) REVERT: C 576 GLN cc_start: 0.4666 (OUTLIER) cc_final: 0.4201 (pp30) REVERT: C 968 MET cc_start: 0.2619 (mmt) cc_final: 0.2377 (mmt) REVERT: C 1003 LYS cc_start: 0.8637 (tptp) cc_final: 0.8372 (tppt) REVERT: C 1015 GLN cc_start: 0.9218 (tp40) cc_final: 0.8436 (tp40) REVERT: C 1047 LYS cc_start: 0.8382 (pttt) cc_final: 0.8119 (ptpp) REVERT: C 1214 LEU cc_start: 0.6610 (tt) cc_final: 0.6218 (pp) REVERT: D 151 MET cc_start: 0.9246 (mtp) cc_final: 0.8967 (ttt) REVERT: D 370 ARG cc_start: 0.9054 (ptm160) cc_final: 0.8702 (ptm160) REVERT: D 385 PHE cc_start: 0.8424 (m-80) cc_final: 0.8192 (m-80) REVERT: D 432 TYR cc_start: 0.9148 (t80) cc_final: 0.8765 (t80) REVERT: D 495 PHE cc_start: 0.7542 (m-80) cc_final: 0.7302 (m-80) REVERT: D 552 ILE cc_start: 0.8680 (mm) cc_final: 0.8391 (mm) REVERT: D 558 TYR cc_start: 0.8870 (m-80) cc_final: 0.8654 (m-80) REVERT: D 571 SER cc_start: 0.9053 (t) cc_final: 0.8814 (p) REVERT: D 597 LEU cc_start: 0.9181 (mt) cc_final: 0.8910 (mt) REVERT: D 743 LEU cc_start: 0.9128 (mp) cc_final: 0.8732 (tt) REVERT: D 841 LYS cc_start: 0.9547 (tptm) cc_final: 0.9322 (tmtt) REVERT: D 916 PHE cc_start: 0.9036 (m-10) cc_final: 0.8721 (m-10) REVERT: D 933 LEU cc_start: 0.9393 (mp) cc_final: 0.9167 (mp) REVERT: D 1109 LEU cc_start: 0.9601 (mt) cc_final: 0.9324 (mt) REVERT: D 1145 TYR cc_start: 0.8330 (m-10) cc_final: 0.7504 (m-10) REVERT: D 1195 HIS cc_start: 0.7104 (t70) cc_final: 0.6477 (t-170) REVERT: D 1248 PHE cc_start: 0.7920 (t80) cc_final: 0.7246 (t80) REVERT: D 1291 GLN cc_start: 0.9316 (pm20) cc_final: 0.9111 (pp30) REVERT: D 1293 ASP cc_start: 0.9606 (m-30) cc_final: 0.8818 (m-30) REVERT: D 1431 PHE cc_start: 0.8770 (p90) cc_final: 0.8432 (p90) outliers start: 3 outliers final: 1 residues processed: 610 average time/residue: 0.5238 time to fit residues: 528.9634 Evaluate side-chains 489 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 486 time to evaluate : 4.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 378 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 436 optimal weight: 20.0000 chunk 289 optimal weight: 4.9990 chunk 516 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 314 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1187 GLN A1302 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN ** C 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS C1302 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43574 Z= 0.215 Angle : 0.776 15.069 59204 Z= 0.386 Chirality : 0.049 0.419 6900 Planarity : 0.005 0.063 7554 Dihedral : 8.098 59.677 6812 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.16 % Favored : 85.73 % Rotamer: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.70 (0.10), residues: 5360 helix: -0.83 (0.17), residues: 816 sheet: -1.94 (0.13), residues: 1466 loop : -3.33 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 741 HIS 0.016 0.001 HIS D1259 PHE 0.034 0.002 PHE B1049 TYR 0.042 0.002 TYR B1104 ARG 0.005 0.001 ARG D1163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 620 time to evaluate : 4.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9377 (tmm) cc_final: 0.9116 (tmm) REVERT: A 34 LEU cc_start: 0.9443 (mt) cc_final: 0.9154 (mp) REVERT: A 55 ASN cc_start: 0.7104 (p0) cc_final: 0.5498 (t0) REVERT: A 121 MET cc_start: 0.9395 (pmm) cc_final: 0.9113 (pmm) REVERT: A 151 MET cc_start: 0.8993 (ttm) cc_final: 0.8162 (tpp) REVERT: A 250 VAL cc_start: 0.9235 (m) cc_final: 0.9013 (p) REVERT: A 263 HIS cc_start: 0.9134 (m-70) cc_final: 0.8890 (t-90) REVERT: A 373 ASP cc_start: 0.9504 (p0) cc_final: 0.9065 (m-30) REVERT: A 415 MET cc_start: 0.7186 (tmm) cc_final: 0.6822 (tmm) REVERT: A 464 MET cc_start: 0.8294 (mtt) cc_final: 0.8009 (mtt) REVERT: A 576 GLN cc_start: 0.4880 (OUTLIER) cc_final: 0.4469 (pp30) REVERT: A 638 ASP cc_start: 0.9202 (t70) cc_final: 0.8914 (t70) REVERT: A 968 MET cc_start: 0.2512 (mmt) cc_final: 0.2224 (mmt) REVERT: A 1003 LYS cc_start: 0.8606 (tptp) cc_final: 0.8324 (tppt) REVERT: A 1040 TRP cc_start: 0.8630 (t60) cc_final: 0.8424 (t60) REVERT: A 1044 PHE cc_start: 0.9586 (m-80) cc_final: 0.9113 (m-80) REVERT: A 1214 LEU cc_start: 0.6659 (tt) cc_final: 0.6332 (pp) REVERT: B 101 MET cc_start: 0.8649 (ttt) cc_final: 0.7931 (ttt) REVERT: B 151 MET cc_start: 0.9251 (mtp) cc_final: 0.8943 (ttt) REVERT: B 194 LEU cc_start: 0.9274 (tp) cc_final: 0.9000 (tp) REVERT: B 223 GLU cc_start: 0.7427 (tp30) cc_final: 0.7199 (tp30) REVERT: B 300 PHE cc_start: 0.8728 (t80) cc_final: 0.8222 (t80) REVERT: B 318 MET cc_start: 0.6867 (ppp) cc_final: 0.6461 (ppp) REVERT: B 370 ARG cc_start: 0.9137 (ptm160) cc_final: 0.8721 (ptm160) REVERT: B 385 PHE cc_start: 0.8470 (m-80) cc_final: 0.8220 (m-80) REVERT: B 404 LEU cc_start: 0.9416 (mt) cc_final: 0.9154 (mt) REVERT: B 432 TYR cc_start: 0.9198 (t80) cc_final: 0.8854 (t80) REVERT: B 571 SER cc_start: 0.8983 (t) cc_final: 0.8769 (p) REVERT: B 597 LEU cc_start: 0.9203 (mt) cc_final: 0.8928 (mt) REVERT: B 743 LEU cc_start: 0.9324 (mp) cc_final: 0.8513 (tp) REVERT: B 841 LYS cc_start: 0.9547 (tptm) cc_final: 0.9323 (tmtt) REVERT: B 916 PHE cc_start: 0.9044 (m-10) cc_final: 0.8778 (m-10) REVERT: B 933 LEU cc_start: 0.9336 (mp) cc_final: 0.9118 (mp) REVERT: B 1044 PHE cc_start: 0.8292 (t80) cc_final: 0.7594 (t80) REVERT: B 1092 LYS cc_start: 0.9343 (mmtm) cc_final: 0.8830 (tmtt) REVERT: B 1104 TYR cc_start: 0.9230 (m-80) cc_final: 0.8950 (m-80) REVERT: B 1109 LEU cc_start: 0.9603 (mt) cc_final: 0.9356 (mt) REVERT: B 1150 LEU cc_start: 0.9409 (mt) cc_final: 0.8762 (mm) REVERT: B 1168 LYS cc_start: 0.9374 (tptt) cc_final: 0.8840 (tptt) REVERT: B 1171 ASN cc_start: 0.9087 (p0) cc_final: 0.8691 (p0) REVERT: B 1209 THR cc_start: 0.8782 (t) cc_final: 0.8521 (t) REVERT: B 1248 PHE cc_start: 0.7909 (t80) cc_final: 0.7284 (t80) REVERT: B 1253 ASP cc_start: 0.8104 (m-30) cc_final: 0.7513 (m-30) REVERT: B 1293 ASP cc_start: 0.9599 (m-30) cc_final: 0.8800 (m-30) REVERT: B 1431 PHE cc_start: 0.8811 (p90) cc_final: 0.8458 (p90) REVERT: C 32 MET cc_start: 0.9377 (tmm) cc_final: 0.9115 (tmm) REVERT: C 34 LEU cc_start: 0.9445 (mt) cc_final: 0.9154 (mp) REVERT: C 55 ASN cc_start: 0.7107 (p0) cc_final: 0.5502 (t0) REVERT: C 121 MET cc_start: 0.9393 (pmm) cc_final: 0.9117 (pmm) REVERT: C 151 MET cc_start: 0.8992 (ttm) cc_final: 0.8163 (tpp) REVERT: C 250 VAL cc_start: 0.9235 (m) cc_final: 0.9016 (p) REVERT: C 373 ASP cc_start: 0.9503 (p0) cc_final: 0.9066 (m-30) REVERT: C 415 MET cc_start: 0.7183 (tmm) cc_final: 0.6819 (tmm) REVERT: C 464 MET cc_start: 0.8185 (mtt) cc_final: 0.7753 (mtt) REVERT: C 1003 LYS cc_start: 0.8616 (tptp) cc_final: 0.8319 (tppt) REVERT: C 1040 TRP cc_start: 0.8628 (t60) cc_final: 0.8424 (t60) REVERT: C 1044 PHE cc_start: 0.9587 (m-80) cc_final: 0.9116 (m-80) REVERT: C 1214 LEU cc_start: 0.6667 (tt) cc_final: 0.6338 (pp) REVERT: D 101 MET cc_start: 0.8653 (ttt) cc_final: 0.7934 (ttt) REVERT: D 151 MET cc_start: 0.9302 (mtp) cc_final: 0.8969 (ttt) REVERT: D 194 LEU cc_start: 0.9271 (tp) cc_final: 0.8998 (tp) REVERT: D 223 GLU cc_start: 0.7423 (tp30) cc_final: 0.7199 (tp30) REVERT: D 300 PHE cc_start: 0.8729 (t80) cc_final: 0.8226 (t80) REVERT: D 318 MET cc_start: 0.6866 (ppp) cc_final: 0.6462 (ppp) REVERT: D 370 ARG cc_start: 0.9137 (ptm160) cc_final: 0.8723 (ptm160) REVERT: D 385 PHE cc_start: 0.8467 (m-80) cc_final: 0.8218 (m-80) REVERT: D 404 LEU cc_start: 0.9418 (mt) cc_final: 0.9152 (mt) REVERT: D 432 TYR cc_start: 0.9199 (t80) cc_final: 0.8855 (t80) REVERT: D 464 MET cc_start: 0.8211 (tmm) cc_final: 0.7114 (tmm) REVERT: D 552 ILE cc_start: 0.8239 (mm) cc_final: 0.7072 (tt) REVERT: D 558 TYR cc_start: 0.8829 (m-80) cc_final: 0.8394 (m-80) REVERT: D 571 SER cc_start: 0.8988 (t) cc_final: 0.8776 (p) REVERT: D 597 LEU cc_start: 0.9210 (mt) cc_final: 0.8936 (mt) REVERT: D 743 LEU cc_start: 0.9329 (mp) cc_final: 0.8510 (tp) REVERT: D 841 LYS cc_start: 0.9547 (tptm) cc_final: 0.9323 (tmtt) REVERT: D 916 PHE cc_start: 0.9050 (m-10) cc_final: 0.8798 (m-10) REVERT: D 933 LEU cc_start: 0.9346 (mp) cc_final: 0.9119 (mp) REVERT: D 997 THR cc_start: 0.8928 (p) cc_final: 0.8607 (t) REVERT: D 1044 PHE cc_start: 0.8316 (t80) cc_final: 0.7755 (t80) REVERT: D 1092 LYS cc_start: 0.9175 (mmpt) cc_final: 0.8867 (tmtt) REVERT: D 1109 LEU cc_start: 0.9571 (mt) cc_final: 0.9282 (mt) REVERT: D 1145 TYR cc_start: 0.8008 (m-10) cc_final: 0.7582 (m-80) REVERT: D 1195 HIS cc_start: 0.7378 (t70) cc_final: 0.6678 (t-170) REVERT: D 1209 THR cc_start: 0.8713 (t) cc_final: 0.8440 (t) REVERT: D 1248 PHE cc_start: 0.7916 (t80) cc_final: 0.7257 (t80) REVERT: D 1293 ASP cc_start: 0.9597 (m-30) cc_final: 0.8789 (m-30) REVERT: D 1389 PHE cc_start: 0.8769 (m-80) cc_final: 0.8255 (m-80) REVERT: D 1431 PHE cc_start: 0.8767 (p90) cc_final: 0.8403 (p90) outliers start: 2 outliers final: 1 residues processed: 621 average time/residue: 0.5236 time to fit residues: 541.7567 Evaluate side-chains 500 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 498 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 101 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 328 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 406 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43574 Z= 0.216 Angle : 0.774 15.478 59204 Z= 0.384 Chirality : 0.049 0.418 6900 Planarity : 0.005 0.062 7554 Dihedral : 8.118 58.992 6812 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 27.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.05 % Favored : 85.84 % Rotamer: Outliers : 0.02 % Allowed : 1.81 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.67 (0.10), residues: 5360 helix: -0.87 (0.17), residues: 818 sheet: -1.86 (0.13), residues: 1436 loop : -3.31 (0.09), residues: 3106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1132 HIS 0.016 0.001 HIS D1259 PHE 0.019 0.002 PHE B 458 TYR 0.038 0.002 TYR B 985 ARG 0.004 0.001 ARG D 598 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 602 time to evaluate : 4.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9352 (tmm) cc_final: 0.9083 (tmm) REVERT: A 34 LEU cc_start: 0.9487 (mt) cc_final: 0.9203 (mp) REVERT: A 55 ASN cc_start: 0.7144 (p0) cc_final: 0.5538 (t0) REVERT: A 121 MET cc_start: 0.9409 (pmm) cc_final: 0.9167 (pmm) REVERT: A 151 MET cc_start: 0.9035 (ttm) cc_final: 0.8191 (tpp) REVERT: A 250 VAL cc_start: 0.9140 (m) cc_final: 0.8915 (p) REVERT: A 263 HIS cc_start: 0.9152 (m-70) cc_final: 0.8871 (t-90) REVERT: A 373 ASP cc_start: 0.9535 (p0) cc_final: 0.9084 (m-30) REVERT: A 464 MET cc_start: 0.8307 (mtt) cc_final: 0.8059 (mtt) REVERT: A 638 ASP cc_start: 0.9246 (t70) cc_final: 0.8947 (t70) REVERT: A 666 MET cc_start: 0.8951 (tpp) cc_final: 0.8616 (tpt) REVERT: A 1003 LYS cc_start: 0.8625 (tptp) cc_final: 0.8343 (tppt) REVERT: A 1040 TRP cc_start: 0.8750 (t60) cc_final: 0.8502 (t60) REVERT: A 1044 PHE cc_start: 0.9543 (m-80) cc_final: 0.9083 (m-80) REVERT: A 1214 LEU cc_start: 0.6749 (tt) cc_final: 0.6378 (pp) REVERT: B 101 MET cc_start: 0.8679 (ttt) cc_final: 0.7970 (ttt) REVERT: B 151 MET cc_start: 0.9283 (mtp) cc_final: 0.8962 (ttt) REVERT: B 194 LEU cc_start: 0.9286 (tp) cc_final: 0.9003 (tp) REVERT: B 223 GLU cc_start: 0.7442 (tp30) cc_final: 0.7220 (tp30) REVERT: B 318 MET cc_start: 0.7014 (ppp) cc_final: 0.6624 (ppp) REVERT: B 370 ARG cc_start: 0.9108 (ptm160) cc_final: 0.8902 (ptm160) REVERT: B 385 PHE cc_start: 0.8505 (m-80) cc_final: 0.8251 (m-80) REVERT: B 432 TYR cc_start: 0.9189 (t80) cc_final: 0.8767 (t80) REVERT: B 500 MET cc_start: 0.1863 (mmm) cc_final: 0.1219 (mmt) REVERT: B 558 TYR cc_start: 0.8744 (m-80) cc_final: 0.8379 (m-80) REVERT: B 597 LEU cc_start: 0.9182 (mt) cc_final: 0.8940 (mt) REVERT: B 841 LYS cc_start: 0.9556 (tptm) cc_final: 0.9320 (tmtt) REVERT: B 916 PHE cc_start: 0.9063 (m-10) cc_final: 0.8744 (m-10) REVERT: B 967 GLN cc_start: 0.8197 (pm20) cc_final: 0.7891 (pm20) REVERT: B 997 THR cc_start: 0.8955 (p) cc_final: 0.8629 (t) REVERT: B 1012 TYR cc_start: 0.9276 (p90) cc_final: 0.8862 (p90) REVERT: B 1092 LYS cc_start: 0.9424 (mmtm) cc_final: 0.8873 (tmtt) REVERT: B 1109 LEU cc_start: 0.9614 (mt) cc_final: 0.9354 (mt) REVERT: B 1145 TYR cc_start: 0.8497 (m-10) cc_final: 0.8118 (m-10) REVERT: B 1195 HIS cc_start: 0.6846 (t-90) cc_final: 0.6450 (t-90) REVERT: B 1209 THR cc_start: 0.8749 (t) cc_final: 0.8480 (t) REVERT: B 1248 PHE cc_start: 0.7946 (t80) cc_final: 0.7325 (t80) REVERT: B 1253 ASP cc_start: 0.7993 (m-30) cc_final: 0.7485 (m-30) REVERT: B 1293 ASP cc_start: 0.9180 (m-30) cc_final: 0.8954 (m-30) REVERT: B 1389 PHE cc_start: 0.8812 (m-80) cc_final: 0.8305 (m-80) REVERT: B 1431 PHE cc_start: 0.8818 (p90) cc_final: 0.8464 (p90) REVERT: C 32 MET cc_start: 0.9381 (tmm) cc_final: 0.9115 (tmm) REVERT: C 34 LEU cc_start: 0.9488 (mt) cc_final: 0.9203 (mp) REVERT: C 55 ASN cc_start: 0.7147 (p0) cc_final: 0.5540 (t0) REVERT: C 121 MET cc_start: 0.9421 (pmm) cc_final: 0.9171 (pmm) REVERT: C 151 MET cc_start: 0.9034 (ttm) cc_final: 0.8193 (tpp) REVERT: C 250 VAL cc_start: 0.9141 (m) cc_final: 0.8918 (p) REVERT: C 373 ASP cc_start: 0.9535 (p0) cc_final: 0.9085 (m-30) REVERT: C 464 MET cc_start: 0.8171 (mtt) cc_final: 0.7722 (mtt) REVERT: C 666 MET cc_start: 0.8953 (tpp) cc_final: 0.8617 (tpt) REVERT: C 1003 LYS cc_start: 0.8572 (tptp) cc_final: 0.8361 (tppt) REVERT: C 1040 TRP cc_start: 0.8744 (t60) cc_final: 0.8487 (t60) REVERT: C 1044 PHE cc_start: 0.9551 (m-80) cc_final: 0.9100 (m-80) REVERT: C 1214 LEU cc_start: 0.6750 (tt) cc_final: 0.6379 (pp) REVERT: D 101 MET cc_start: 0.8684 (ttt) cc_final: 0.7974 (ttt) REVERT: D 151 MET cc_start: 0.9329 (mtp) cc_final: 0.8954 (ttt) REVERT: D 194 LEU cc_start: 0.9281 (tp) cc_final: 0.8997 (tp) REVERT: D 223 GLU cc_start: 0.7442 (tp30) cc_final: 0.7228 (tp30) REVERT: D 318 MET cc_start: 0.7041 (ppp) cc_final: 0.6797 (ppp) REVERT: D 370 ARG cc_start: 0.9113 (ptm160) cc_final: 0.8909 (ptm160) REVERT: D 385 PHE cc_start: 0.8506 (m-80) cc_final: 0.8252 (m-80) REVERT: D 432 TYR cc_start: 0.9189 (t80) cc_final: 0.8767 (t80) REVERT: D 500 MET cc_start: 0.1872 (mmm) cc_final: 0.1232 (mmt) REVERT: D 552 ILE cc_start: 0.8405 (mm) cc_final: 0.8149 (mm) REVERT: D 597 LEU cc_start: 0.9189 (mt) cc_final: 0.8950 (mt) REVERT: D 841 LYS cc_start: 0.9556 (tptm) cc_final: 0.9320 (tmtt) REVERT: D 916 PHE cc_start: 0.9071 (m-10) cc_final: 0.8751 (m-10) REVERT: D 967 GLN cc_start: 0.8151 (pm20) cc_final: 0.7891 (pm20) REVERT: D 997 THR cc_start: 0.8955 (p) cc_final: 0.8635 (t) REVERT: D 1012 TYR cc_start: 0.9306 (p90) cc_final: 0.8879 (p90) REVERT: D 1092 LYS cc_start: 0.9266 (mmpt) cc_final: 0.9023 (mmmt) REVERT: D 1109 LEU cc_start: 0.9598 (mt) cc_final: 0.9364 (mt) REVERT: D 1145 TYR cc_start: 0.8062 (m-10) cc_final: 0.7745 (m-80) REVERT: D 1195 HIS cc_start: 0.7352 (t70) cc_final: 0.6567 (t-170) REVERT: D 1209 THR cc_start: 0.8787 (t) cc_final: 0.8501 (t) REVERT: D 1248 PHE cc_start: 0.7936 (t80) cc_final: 0.7315 (t80) REVERT: D 1253 ASP cc_start: 0.8056 (m-30) cc_final: 0.7511 (m-30) REVERT: D 1293 ASP cc_start: 0.9173 (m-30) cc_final: 0.8947 (m-30) REVERT: D 1389 PHE cc_start: 0.8760 (m-80) cc_final: 0.8263 (m-80) REVERT: D 1431 PHE cc_start: 0.8770 (p90) cc_final: 0.8409 (p90) outliers start: 1 outliers final: 1 residues processed: 603 average time/residue: 0.5143 time to fit residues: 517.7296 Evaluate side-chains 492 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 491 time to evaluate : 4.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 1.9990 chunk 494 optimal weight: 7.9990 chunk 451 optimal weight: 10.0000 chunk 481 optimal weight: 0.3980 chunk 289 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 378 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 435 optimal weight: 6.9990 chunk 455 optimal weight: 8.9990 chunk 479 optimal weight: 8.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 ASN ** B 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN D1015 GLN ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 43574 Z= 0.269 Angle : 0.821 14.798 59204 Z= 0.412 Chirality : 0.050 0.429 6900 Planarity : 0.006 0.060 7554 Dihedral : 8.752 88.799 6812 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 34.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.34 % Favored : 84.55 % Rotamer: Outliers : 0.02 % Allowed : 1.17 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.76 (0.10), residues: 5360 helix: -1.03 (0.17), residues: 818 sheet: -1.95 (0.13), residues: 1444 loop : -3.34 (0.10), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B1132 HIS 0.017 0.002 HIS D1259 PHE 0.030 0.002 PHE D1049 TYR 0.040 0.002 TYR B 985 ARG 0.005 0.001 ARG B1122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 579 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9448 (mt) cc_final: 0.9227 (mp) REVERT: A 55 ASN cc_start: 0.7218 (p0) cc_final: 0.5661 (t0) REVERT: A 121 MET cc_start: 0.9402 (pmm) cc_final: 0.9147 (pmm) REVERT: A 151 MET cc_start: 0.9117 (ttm) cc_final: 0.8290 (tpp) REVERT: A 373 ASP cc_start: 0.9602 (p0) cc_final: 0.9175 (m-30) REVERT: A 464 MET cc_start: 0.8205 (mtt) cc_final: 0.7916 (mtt) REVERT: A 638 ASP cc_start: 0.9295 (t70) cc_final: 0.9008 (t70) REVERT: A 1044 PHE cc_start: 0.9566 (m-80) cc_final: 0.9120 (m-80) REVERT: A 1214 LEU cc_start: 0.6917 (tt) cc_final: 0.6489 (pp) REVERT: B 101 MET cc_start: 0.8724 (ttt) cc_final: 0.8030 (ttt) REVERT: B 151 MET cc_start: 0.9311 (mtp) cc_final: 0.8998 (ttt) REVERT: B 194 LEU cc_start: 0.9304 (tp) cc_final: 0.9039 (tp) REVERT: B 223 GLU cc_start: 0.7405 (tp30) cc_final: 0.7139 (tp30) REVERT: B 318 MET cc_start: 0.7141 (ppp) cc_final: 0.6906 (ppp) REVERT: B 385 PHE cc_start: 0.8620 (m-80) cc_final: 0.8368 (m-80) REVERT: B 432 TYR cc_start: 0.9194 (t80) cc_final: 0.8818 (t80) REVERT: B 552 ILE cc_start: 0.8871 (mm) cc_final: 0.8657 (mm) REVERT: B 558 TYR cc_start: 0.8828 (m-80) cc_final: 0.8577 (m-80) REVERT: B 586 ARG cc_start: 0.8784 (ttt180) cc_final: 0.8183 (tpt90) REVERT: B 597 LEU cc_start: 0.9263 (mt) cc_final: 0.9027 (mt) REVERT: B 786 LEU cc_start: 0.7705 (tp) cc_final: 0.7468 (tp) REVERT: B 916 PHE cc_start: 0.9070 (m-10) cc_final: 0.8846 (m-10) REVERT: B 933 LEU cc_start: 0.9395 (mp) cc_final: 0.9183 (mp) REVERT: B 997 THR cc_start: 0.9039 (p) cc_final: 0.8745 (t) REVERT: B 1109 LEU cc_start: 0.9676 (mt) cc_final: 0.9402 (mt) REVERT: B 1195 HIS cc_start: 0.6976 (t-90) cc_final: 0.6592 (t-90) REVERT: B 1208 MET cc_start: 0.9447 (ppp) cc_final: 0.9237 (ppp) REVERT: B 1362 GLN cc_start: 0.9273 (pt0) cc_final: 0.8775 (pm20) REVERT: B 1431 PHE cc_start: 0.8861 (p90) cc_final: 0.8521 (p90) REVERT: C 34 LEU cc_start: 0.9448 (mt) cc_final: 0.9226 (mp) REVERT: C 55 ASN cc_start: 0.7220 (p0) cc_final: 0.5664 (t0) REVERT: C 121 MET cc_start: 0.9399 (pmm) cc_final: 0.9149 (pmm) REVERT: C 151 MET cc_start: 0.9115 (ttm) cc_final: 0.8285 (tpp) REVERT: C 373 ASP cc_start: 0.9602 (p0) cc_final: 0.9177 (m-30) REVERT: C 464 MET cc_start: 0.8172 (mtt) cc_final: 0.7669 (mtt) REVERT: C 968 MET cc_start: 0.1914 (mmt) cc_final: 0.1554 (mmt) REVERT: C 1003 LYS cc_start: 0.8728 (tptp) cc_final: 0.8431 (tppt) REVERT: C 1015 GLN cc_start: 0.9217 (tp40) cc_final: 0.8509 (tp40) REVERT: C 1040 TRP cc_start: 0.8828 (t60) cc_final: 0.8626 (t60) REVERT: C 1044 PHE cc_start: 0.9551 (m-80) cc_final: 0.9096 (m-80) REVERT: C 1214 LEU cc_start: 0.6921 (tt) cc_final: 0.6499 (pp) REVERT: D 101 MET cc_start: 0.8726 (ttt) cc_final: 0.8033 (ttt) REVERT: D 151 MET cc_start: 0.9318 (mtp) cc_final: 0.8995 (ttt) REVERT: D 194 LEU cc_start: 0.9302 (tp) cc_final: 0.9034 (tp) REVERT: D 223 GLU cc_start: 0.7406 (tp30) cc_final: 0.7146 (tp30) REVERT: D 318 MET cc_start: 0.7242 (ppp) cc_final: 0.7017 (ppp) REVERT: D 385 PHE cc_start: 0.8619 (m-80) cc_final: 0.8369 (m-80) REVERT: D 432 TYR cc_start: 0.9194 (t80) cc_final: 0.8819 (t80) REVERT: D 464 MET cc_start: 0.8280 (tmm) cc_final: 0.7276 (tmm) REVERT: D 552 ILE cc_start: 0.8730 (mm) cc_final: 0.7431 (tt) REVERT: D 558 TYR cc_start: 0.8744 (m-80) cc_final: 0.8333 (m-80) REVERT: D 586 ARG cc_start: 0.8788 (ttt180) cc_final: 0.8175 (tpt90) REVERT: D 597 LEU cc_start: 0.9269 (mt) cc_final: 0.9035 (mt) REVERT: D 786 LEU cc_start: 0.7611 (tp) cc_final: 0.7354 (tp) REVERT: D 916 PHE cc_start: 0.9101 (m-10) cc_final: 0.8868 (m-10) REVERT: D 933 LEU cc_start: 0.9391 (mp) cc_final: 0.9175 (mp) REVERT: D 997 THR cc_start: 0.9030 (p) cc_final: 0.8724 (t) REVERT: D 1012 TYR cc_start: 0.9311 (p90) cc_final: 0.8899 (p90) REVERT: D 1092 LYS cc_start: 0.9392 (mmpt) cc_final: 0.9143 (mmmt) REVERT: D 1109 LEU cc_start: 0.9664 (mt) cc_final: 0.9405 (mt) REVERT: D 1145 TYR cc_start: 0.8118 (m-10) cc_final: 0.7853 (m-10) REVERT: D 1195 HIS cc_start: 0.7359 (t70) cc_final: 0.6903 (t70) REVERT: D 1208 MET cc_start: 0.9416 (ppp) cc_final: 0.9211 (ppp) REVERT: D 1248 PHE cc_start: 0.8022 (t80) cc_final: 0.7406 (t80) REVERT: D 1253 ASP cc_start: 0.8160 (m-30) cc_final: 0.7593 (m-30) REVERT: D 1362 GLN cc_start: 0.9249 (pt0) cc_final: 0.8757 (pm20) REVERT: D 1389 PHE cc_start: 0.8691 (m-80) cc_final: 0.8252 (m-80) REVERT: D 1431 PHE cc_start: 0.8760 (p90) cc_final: 0.8428 (p90) outliers start: 1 outliers final: 1 residues processed: 580 average time/residue: 0.5258 time to fit residues: 509.8110 Evaluate side-chains 461 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 460 time to evaluate : 4.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 316 optimal weight: 7.9990 chunk 509 optimal weight: 7.9990 chunk 310 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 chunk 533 optimal weight: 10.0000 chunk 491 optimal weight: 10.0000 chunk 425 optimal weight: 0.0070 chunk 44 optimal weight: 20.0000 chunk 328 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1171 ASN ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43574 Z= 0.240 Angle : 0.802 15.349 59204 Z= 0.400 Chirality : 0.051 0.417 6900 Planarity : 0.005 0.060 7554 Dihedral : 9.035 107.568 6812 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 30.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.51 % Favored : 85.37 % Rotamer: Outliers : 0.02 % Allowed : 0.53 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.69 (0.10), residues: 5360 helix: -0.97 (0.17), residues: 816 sheet: -1.90 (0.14), residues: 1344 loop : -3.27 (0.09), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D1132 HIS 0.014 0.001 HIS D1259 PHE 0.039 0.002 PHE D1049 TYR 0.038 0.002 TYR B 985 ARG 0.009 0.001 ARG D 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 571 time to evaluate : 4.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7215 (p0) cc_final: 0.5663 (t0) REVERT: A 121 MET cc_start: 0.9407 (pmm) cc_final: 0.9172 (pmm) REVERT: A 151 MET cc_start: 0.9065 (ttm) cc_final: 0.8237 (tpp) REVERT: A 250 VAL cc_start: 0.9112 (t) cc_final: 0.8893 (p) REVERT: A 373 ASP cc_start: 0.9579 (p0) cc_final: 0.9145 (m-30) REVERT: A 968 MET cc_start: 0.1428 (mmt) cc_final: 0.0916 (mmt) REVERT: A 1003 LYS cc_start: 0.8713 (tptp) cc_final: 0.8383 (tptt) REVERT: A 1214 LEU cc_start: 0.6889 (tt) cc_final: 0.6493 (pp) REVERT: B 101 MET cc_start: 0.8749 (ttt) cc_final: 0.8054 (ttt) REVERT: B 151 MET cc_start: 0.9348 (mtp) cc_final: 0.8960 (ttt) REVERT: B 194 LEU cc_start: 0.9309 (tp) cc_final: 0.9058 (tp) REVERT: B 223 GLU cc_start: 0.7405 (tp30) cc_final: 0.7147 (tp30) REVERT: B 385 PHE cc_start: 0.8560 (m-80) cc_final: 0.8323 (m-80) REVERT: B 432 TYR cc_start: 0.9209 (t80) cc_final: 0.8826 (t80) REVERT: B 500 MET cc_start: 0.2500 (mmm) cc_final: 0.1816 (mmt) REVERT: B 586 ARG cc_start: 0.8739 (ttt180) cc_final: 0.8166 (tpt90) REVERT: B 597 LEU cc_start: 0.9225 (mt) cc_final: 0.9003 (mt) REVERT: B 916 PHE cc_start: 0.9016 (m-10) cc_final: 0.8773 (m-10) REVERT: B 933 LEU cc_start: 0.9374 (mp) cc_final: 0.9139 (mp) REVERT: B 997 THR cc_start: 0.9072 (p) cc_final: 0.8772 (t) REVERT: B 1109 LEU cc_start: 0.9664 (mt) cc_final: 0.9429 (mt) REVERT: B 1195 HIS cc_start: 0.6954 (t-90) cc_final: 0.6564 (t-90) REVERT: B 1353 ASP cc_start: 0.8207 (m-30) cc_final: 0.7657 (p0) REVERT: B 1362 GLN cc_start: 0.9280 (pt0) cc_final: 0.8774 (pm20) REVERT: B 1389 PHE cc_start: 0.8748 (m-80) cc_final: 0.8262 (m-80) REVERT: B 1431 PHE cc_start: 0.8887 (p90) cc_final: 0.8615 (p90) REVERT: C 55 ASN cc_start: 0.7214 (p0) cc_final: 0.5663 (t0) REVERT: C 121 MET cc_start: 0.9404 (pmm) cc_final: 0.9172 (pmm) REVERT: C 151 MET cc_start: 0.9065 (ttm) cc_final: 0.8235 (tpp) REVERT: C 250 VAL cc_start: 0.9125 (t) cc_final: 0.8906 (p) REVERT: C 373 ASP cc_start: 0.9586 (p0) cc_final: 0.9162 (m-30) REVERT: C 464 MET cc_start: 0.8153 (mtt) cc_final: 0.7653 (mtt) REVERT: C 968 MET cc_start: 0.1881 (mmt) cc_final: 0.1522 (mmt) REVERT: C 1003 LYS cc_start: 0.8699 (tptp) cc_final: 0.8395 (tppt) REVERT: C 1044 PHE cc_start: 0.9566 (m-80) cc_final: 0.9097 (m-80) REVERT: C 1214 LEU cc_start: 0.6894 (tt) cc_final: 0.6498 (pp) REVERT: D 101 MET cc_start: 0.8753 (ttt) cc_final: 0.8058 (ttt) REVERT: D 151 MET cc_start: 0.9376 (mtp) cc_final: 0.9003 (ttt) REVERT: D 194 LEU cc_start: 0.9305 (tp) cc_final: 0.9054 (tp) REVERT: D 223 GLU cc_start: 0.7406 (tp30) cc_final: 0.7145 (tp30) REVERT: D 385 PHE cc_start: 0.8559 (m-80) cc_final: 0.8323 (m-80) REVERT: D 432 TYR cc_start: 0.9209 (t80) cc_final: 0.8827 (t80) REVERT: D 464 MET cc_start: 0.8208 (tmm) cc_final: 0.7236 (tmm) REVERT: D 500 MET cc_start: 0.2478 (mmm) cc_final: 0.1868 (mmt) REVERT: D 558 TYR cc_start: 0.8728 (m-80) cc_final: 0.8399 (m-80) REVERT: D 586 ARG cc_start: 0.8735 (ttt180) cc_final: 0.8159 (tpt90) REVERT: D 597 LEU cc_start: 0.9228 (mt) cc_final: 0.8997 (mt) REVERT: D 916 PHE cc_start: 0.9021 (m-10) cc_final: 0.8773 (m-10) REVERT: D 933 LEU cc_start: 0.9367 (mp) cc_final: 0.9129 (mp) REVERT: D 997 THR cc_start: 0.9217 (p) cc_final: 0.8946 (t) REVERT: D 1012 TYR cc_start: 0.9294 (p90) cc_final: 0.8872 (p90) REVERT: D 1092 LYS cc_start: 0.9396 (mmpt) cc_final: 0.9145 (mmmt) REVERT: D 1109 LEU cc_start: 0.9643 (mt) cc_final: 0.9423 (mt) REVERT: D 1195 HIS cc_start: 0.7464 (t70) cc_final: 0.6724 (t-170) REVERT: D 1208 MET cc_start: 0.9384 (ppp) cc_final: 0.9174 (ppp) REVERT: D 1353 ASP cc_start: 0.8207 (m-30) cc_final: 0.7660 (p0) REVERT: D 1362 GLN cc_start: 0.9274 (pt0) cc_final: 0.8772 (pm20) REVERT: D 1389 PHE cc_start: 0.8704 (m-80) cc_final: 0.8238 (m-80) REVERT: D 1431 PHE cc_start: 0.8814 (p90) cc_final: 0.8503 (p90) outliers start: 1 outliers final: 1 residues processed: 572 average time/residue: 0.5187 time to fit residues: 498.1682 Evaluate side-chains 452 residues out of total 4702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 5.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 6.9990 chunk 452 optimal weight: 10.0000 chunk 130 optimal weight: 0.3980 chunk 392 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 118 optimal weight: 40.0000 chunk 425 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 437 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1182 HIS ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1171 ASN ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1182 HIS ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.092715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.068626 restraints weight = 285633.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.070516 restraints weight = 217550.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.071895 restraints weight = 176682.901| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 43574 Z= 0.213 Angle : 0.777 15.446 59204 Z= 0.386 Chirality : 0.050 0.404 6900 Planarity : 0.005 0.061 7554 Dihedral : 8.899 106.362 6812 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.24 % Favored : 85.65 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.63 (0.10), residues: 5360 helix: -0.92 (0.17), residues: 816 sheet: -1.87 (0.14), residues: 1284 loop : -3.22 (0.09), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1040 HIS 0.012 0.001 HIS D1259 PHE 0.033 0.002 PHE D 359 TYR 0.036 0.002 TYR B 985 ARG 0.003 0.000 ARG C 270 =============================================================================== Job complete usr+sys time: 9913.93 seconds wall clock time: 181 minutes 27.01 seconds (10887.01 seconds total)