Starting phenix.real_space_refine on Tue Mar 26 10:34:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/03_2024/6gsi_0056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/03_2024/6gsi_0056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/03_2024/6gsi_0056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/03_2024/6gsi_0056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/03_2024/6gsi_0056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/03_2024/6gsi_0056.pdb" } resolution = 3.75 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= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians K 12 8.98 5 S 264 5.16 5 C 48201 2.51 5 N 12891 2.21 5 O 14763 1.98 5 H 74247 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 550": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 641": "OE1" <-> "OE2" Residue "B ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 663": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 641": "OE1" <-> "OE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 550": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 641": "OE1" <-> "OE2" Residue "N ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 663": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 641": "OE1" <-> "OE2" Residue "P PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 550": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y GLU 641": "OE1" <-> "OE2" Residue "Z ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 663": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 GLU 641": "OE1" <-> "OE2" Residue "1 PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "9 ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "9 ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150378 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8123 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 31, 'TRANS': 502} Chain: "B" Number of atoms: 8061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8061 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 30, 'TRANS': 499} Chain: "C" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8121 Classifications: {'peptide': 534} Link IDs: {'CIS': 2, 'PTRANS': 31, 'TRANS': 500} Chain: "D" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8123 Classifications: {'peptide': 534} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 501} Chain: "E" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3023 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 186} Chain: "F" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3033 Classifications: {'peptide': 202} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 187} Chain: "G" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3013 Classifications: {'peptide': 200} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 185} Chain: "H" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3008 Classifications: {'peptide': 200} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 185} Chain: "I" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "J" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1467 Classifications: {'peptide': 89} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 85} Chain: "K" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "L" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1468 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8123 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 31, 'TRANS': 502} Chain: "N" Number of atoms: 8061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8061 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 30, 'TRANS': 499} Chain: "O" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8121 Classifications: {'peptide': 534} Link IDs: {'CIS': 2, 'PTRANS': 31, 'TRANS': 500} Chain: "P" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8123 Classifications: {'peptide': 534} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 501} Chain: "Q" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3023 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 186} Chain: "R" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3033 Classifications: {'peptide': 202} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 187} Chain: "S" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3013 Classifications: {'peptide': 200} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 185} Chain: "T" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3008 Classifications: {'peptide': 200} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 185} Chain: "U" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "V" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1467 Classifications: {'peptide': 89} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 85} Chain: "W" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "X" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1468 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8123 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 31, 'TRANS': 502} Chain: "Z" Number of atoms: 8061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8061 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 30, 'TRANS': 499} Chain: "0" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8121 Classifications: {'peptide': 534} Link IDs: {'CIS': 2, 'PTRANS': 31, 'TRANS': 500} Chain: "1" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8123 Classifications: {'peptide': 534} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 501} Chain: "2" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3023 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 186} Chain: "3" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3033 Classifications: {'peptide': 202} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 187} Chain: "4" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3013 Classifications: {'peptide': 200} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 185} Chain: "5" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3008 Classifications: {'peptide': 200} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 185} Chain: "6" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "7" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1467 Classifications: {'peptide': 89} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 85} Chain: "8" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "9" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1468 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 48.52, per 1000 atoms: 0.32 Number of scatterers: 150378 At special positions: 0 Unit cell: (206.61, 246.015, 185.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 12 19.00 S 264 16.00 O 14763 8.00 N 12891 7.00 C 48201 6.00 H 74247 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 211 " distance=2.04 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 211 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 211 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 49 " - pdb=" SG CYS Q 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 211 " distance=2.04 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 211 " distance=2.03 Simple disulfide: pdb=" SG CYS S 49 " - pdb=" SG CYS S 108 " distance=2.03 Simple disulfide: pdb=" SG CYS S 152 " - pdb=" SG CYS S 211 " distance=2.03 Simple disulfide: pdb=" SG CYS T 49 " - pdb=" SG CYS T 108 " distance=2.03 Simple disulfide: pdb=" SG CYS T 152 " - pdb=" SG CYS T 211 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 49 " - pdb=" SG CYS 2 108 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 152 " - pdb=" SG CYS 2 211 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 49 " - pdb=" SG CYS 3 108 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 152 " - pdb=" SG CYS 3 211 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 49 " - pdb=" SG CYS 4 108 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 152 " - pdb=" SG CYS 4 211 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 49 " - pdb=" SG CYS 5 108 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 152 " - pdb=" SG CYS 5 211 " 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 Time building additional restraints: 101.13 Conformation dependent library (CDL) restraints added in 11.4 seconds 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18150 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 0 sheets defined 15.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 199 through 206 removed outlier: 3.661A pdb=" N HIS A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.555A pdb=" N LEU A 349 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 588 through 598 removed outlier: 3.513A pdb=" N GLN A 594 " --> pdb=" O HIS A 590 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 595 " --> pdb=" O THR A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.564A pdb=" N LEU B 198 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 4.049A pdb=" N LYS B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 544 through 548 removed outlier: 3.847A pdb=" N VAL B 548 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 removed outlier: 3.938A pdb=" N GLN B 594 " --> pdb=" O HIS B 590 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU B 595 " --> pdb=" O THR B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.597A pdb=" N SER C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 155 " --> pdb=" O MET C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 removed outlier: 4.083A pdb=" N PHE C 170 " --> pdb=" O TRP C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.767A pdb=" N LEU C 198 " --> pdb=" O GLY C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 448 through 455 removed outlier: 3.787A pdb=" N TYR C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 598 removed outlier: 3.966A pdb=" N LEU C 595 " --> pdb=" O THR C 591 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 597 " --> pdb=" O ARG C 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 159 removed outlier: 3.534A pdb=" N ALA D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 removed outlier: 4.157A pdb=" N PHE D 170 " --> pdb=" O TRP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 removed outlier: 3.846A pdb=" N LEU D 198 " --> pdb=" O GLY D 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 195 through 198' Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 448 through 454 Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 588 through 598 removed outlier: 3.600A pdb=" N LEU D 597 " --> pdb=" O ARG D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.876A pdb=" N THR E 206 " --> pdb=" O ALA E 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 103 Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 99 through 103 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 202 through 206 Processing helix chain 'I' and resid 20 through 27 Processing helix chain 'I' and resid 30 through 52 removed outlier: 3.662A pdb=" N LEU I 46 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU I 51 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 75 removed outlier: 3.776A pdb=" N LEU I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU I 58 " --> pdb=" O ASN I 54 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 4.190A pdb=" N ALA I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA I 74 " --> pdb=" O LEU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 94 removed outlier: 5.165A pdb=" N GLN I 92 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN I 94 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 62 removed outlier: 3.845A pdb=" N ASP J 24 " --> pdb=" O GLN J 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU J 28 " --> pdb=" O ASP J 24 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY J 29 " --> pdb=" O LYS J 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP J 42 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN J 47 " --> pdb=" O HIS J 43 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN J 48 " --> pdb=" O GLN J 44 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL J 50 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS J 55 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU J 57 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU J 58 " --> pdb=" O ASN J 54 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG J 60 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 72 removed outlier: 3.984A pdb=" N LEU J 70 " --> pdb=" O GLN J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 105 removed outlier: 3.598A pdb=" N LEU J 103 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE J 104 " --> pdb=" O TYR J 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 27 Processing helix chain 'K' and resid 30 through 60 removed outlier: 3.753A pdb=" N LYS K 37 " --> pdb=" O GLU K 33 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN K 44 " --> pdb=" O LYS K 40 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE K 56 " --> pdb=" O GLN K 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU K 57 " --> pdb=" O PHE K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 75 removed outlier: 3.921A pdb=" N ALA K 74 " --> pdb=" O LEU K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 25 through 62 removed outlier: 3.814A pdb=" N ALA L 35 " --> pdb=" O GLN L 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU L 46 " --> pdb=" O ASP L 42 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE L 56 " --> pdb=" O GLN L 52 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN L 59 " --> pdb=" O LYS L 55 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 72 Processing helix chain 'L' and resid 89 through 105 removed outlier: 3.558A pdb=" N PHE L 104 " --> pdb=" O TYR L 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 160 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 206 removed outlier: 3.660A pdb=" N HIS M 204 " --> pdb=" O PRO M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 252 Processing helix chain 'M' and resid 346 through 350 removed outlier: 3.556A pdb=" N LEU M 349 " --> pdb=" O SER M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 544 through 548 Processing helix chain 'M' and resid 588 through 598 removed outlier: 3.513A pdb=" N GLN M 594 " --> pdb=" O HIS M 590 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU M 595 " --> pdb=" O THR M 591 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 157 Processing helix chain 'N' and resid 195 through 199 removed outlier: 3.564A pdb=" N LEU N 198 " --> pdb=" O GLY N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 207 removed outlier: 4.049A pdb=" N LYS N 207 " --> pdb=" O GLU N 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 251 Processing helix chain 'N' and resid 544 through 548 removed outlier: 3.846A pdb=" N VAL N 548 " --> pdb=" O ARG N 545 " (cutoff:3.500A) Processing helix chain 'N' and resid 588 through 595 removed outlier: 3.938A pdb=" N GLN N 594 " --> pdb=" O HIS N 590 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU N 595 " --> pdb=" O THR N 591 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 159 removed outlier: 3.598A pdb=" N SER O 152 " --> pdb=" O SER O 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 153 " --> pdb=" O ALA O 149 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA O 154 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA O 155 " --> pdb=" O MET O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 170 removed outlier: 4.084A pdb=" N PHE O 170 " --> pdb=" O TRP O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 198 removed outlier: 3.767A pdb=" N LEU O 198 " --> pdb=" O GLY O 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 195 through 198' Processing helix chain 'O' and resid 199 through 206 Processing helix chain 'O' and resid 246 through 251 Processing helix chain 'O' and resid 448 through 455 removed outlier: 3.788A pdb=" N TYR O 452 " --> pdb=" O THR O 448 " (cutoff:3.500A) Processing helix chain 'O' and resid 588 through 598 removed outlier: 3.966A pdb=" N LEU O 595 " --> pdb=" O THR O 591 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU O 597 " --> pdb=" O ARG O 593 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 159 removed outlier: 3.534A pdb=" N ALA P 154 " --> pdb=" O GLN P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 170 removed outlier: 4.157A pdb=" N PHE P 170 " --> pdb=" O TRP P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 198 removed outlier: 3.846A pdb=" N LEU P 198 " --> pdb=" O GLY P 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 195 through 198' Processing helix chain 'P' and resid 199 through 206 Processing helix chain 'P' and resid 246 through 251 Processing helix chain 'P' and resid 448 through 454 Processing helix chain 'P' and resid 544 through 548 Processing helix chain 'P' and resid 588 through 598 removed outlier: 3.600A pdb=" N LEU P 597 " --> pdb=" O ARG P 593 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 103 Processing helix chain 'Q' and resid 202 through 206 removed outlier: 3.875A pdb=" N THR Q 206 " --> pdb=" O ALA Q 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 103 Processing helix chain 'S' and resid 82 through 84 No H-bonds generated for 'chain 'S' and resid 82 through 84' Processing helix chain 'S' and resid 99 through 103 Processing helix chain 'T' and resid 99 through 103 Processing helix chain 'T' and resid 202 through 206 Processing helix chain 'U' and resid 20 through 27 Processing helix chain 'U' and resid 30 through 52 removed outlier: 3.661A pdb=" N LEU U 46 " --> pdb=" O ASP U 42 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU U 51 " --> pdb=" O ASN U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 75 removed outlier: 3.776A pdb=" N LEU U 57 " --> pdb=" O PHE U 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU U 58 " --> pdb=" O ASN U 54 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL U 61 " --> pdb=" O LEU U 57 " (cutoff:3.500A) Proline residue: U 64 - end of helix removed outlier: 4.190A pdb=" N ALA U 73 " --> pdb=" O ARG U 69 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA U 74 " --> pdb=" O LEU U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 94 removed outlier: 5.165A pdb=" N GLN U 92 " --> pdb=" O TYR U 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN U 94 " --> pdb=" O ASP U 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 62 removed outlier: 3.844A pdb=" N ASP V 24 " --> pdb=" O GLN V 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA V 26 " --> pdb=" O GLU V 22 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU V 28 " --> pdb=" O ASP V 24 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU V 36 " --> pdb=" O ARG V 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS V 37 " --> pdb=" O GLU V 33 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP V 42 " --> pdb=" O ARG V 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN V 47 " --> pdb=" O HIS V 43 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN V 48 " --> pdb=" O GLN V 44 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL V 50 " --> pdb=" O LEU V 46 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS V 55 " --> pdb=" O GLU V 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU V 57 " --> pdb=" O PHE V 53 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU V 58 " --> pdb=" O ASN V 54 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG V 60 " --> pdb=" O ILE V 56 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL V 61 " --> pdb=" O LEU V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 72 removed outlier: 3.983A pdb=" N LEU V 70 " --> pdb=" O GLN V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 105 removed outlier: 3.598A pdb=" N LEU V 103 " --> pdb=" O SER V 99 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE V 104 " --> pdb=" O TYR V 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 27 Processing helix chain 'W' and resid 30 through 60 removed outlier: 3.754A pdb=" N LYS W 37 " --> pdb=" O GLU W 33 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN W 44 " --> pdb=" O LYS W 40 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN W 49 " --> pdb=" O ALA W 45 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU W 51 " --> pdb=" O ASN W 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE W 56 " --> pdb=" O GLN W 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU W 57 " --> pdb=" O PHE W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 75 removed outlier: 3.921A pdb=" N ALA W 74 " --> pdb=" O LEU W 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 87 through 91 Processing helix chain 'X' and resid 19 through 23 Processing helix chain 'X' and resid 25 through 62 removed outlier: 3.814A pdb=" N ALA X 35 " --> pdb=" O GLN X 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG X 38 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU X 46 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS X 55 " --> pdb=" O GLU X 51 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE X 56 " --> pdb=" O GLN X 52 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN X 59 " --> pdb=" O LYS X 55 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG X 60 " --> pdb=" O ILE X 56 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL X 61 " --> pdb=" O LEU X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 72 Processing helix chain 'X' and resid 89 through 105 removed outlier: 3.558A pdb=" N PHE X 104 " --> pdb=" O TYR X 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 151 through 160 Processing helix chain 'Y' and resid 195 through 198 Processing helix chain 'Y' and resid 199 through 206 removed outlier: 3.661A pdb=" N HIS Y 204 " --> pdb=" O PRO Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 247 through 252 Processing helix chain 'Y' and resid 346 through 350 removed outlier: 3.555A pdb=" N LEU Y 349 " --> pdb=" O SER Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 548 Processing helix chain 'Y' and resid 588 through 598 removed outlier: 3.513A pdb=" N GLN Y 594 " --> pdb=" O HIS Y 590 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU Y 595 " --> pdb=" O THR Y 591 " (cutoff:3.500A) Processing helix chain 'Z' and resid 150 through 157 Processing helix chain 'Z' and resid 195 through 199 removed outlier: 3.564A pdb=" N LEU Z 198 " --> pdb=" O GLY Z 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 201 through 207 removed outlier: 4.049A pdb=" N LYS Z 207 " --> pdb=" O GLU Z 203 " (cutoff:3.500A) Processing helix chain 'Z' and resid 247 through 251 Processing helix chain 'Z' and resid 544 through 548 removed outlier: 3.847A pdb=" N VAL Z 548 " --> pdb=" O ARG Z 545 " (cutoff:3.500A) Processing helix chain 'Z' and resid 588 through 595 removed outlier: 3.938A pdb=" N GLN Z 594 " --> pdb=" O HIS Z 590 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU Z 595 " --> pdb=" O THR Z 591 " (cutoff:3.500A) Processing helix chain '0' and resid 148 through 159 removed outlier: 3.598A pdb=" N SER 0 152 " --> pdb=" O SER 0 148 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 0 153 " --> pdb=" O ALA 0 149 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA 0 154 " --> pdb=" O GLN 0 150 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA 0 155 " --> pdb=" O MET 0 151 " (cutoff:3.500A) Processing helix chain '0' and resid 165 through 170 removed outlier: 4.083A pdb=" N PHE 0 170 " --> pdb=" O TRP 0 167 " (cutoff:3.500A) Processing helix chain '0' and resid 195 through 198 removed outlier: 3.767A pdb=" N LEU 0 198 " --> pdb=" O GLY 0 195 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 195 through 198' Processing helix chain '0' and resid 199 through 206 Processing helix chain '0' and resid 246 through 251 Processing helix chain '0' and resid 448 through 455 removed outlier: 3.787A pdb=" N TYR 0 452 " --> pdb=" O THR 0 448 " (cutoff:3.500A) Processing helix chain '0' and resid 588 through 598 removed outlier: 3.966A pdb=" N LEU 0 595 " --> pdb=" O THR 0 591 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU 0 597 " --> pdb=" O ARG 0 593 " (cutoff:3.500A) Processing helix chain '1' and resid 148 through 159 removed outlier: 3.535A pdb=" N ALA 1 154 " --> pdb=" O GLN 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 170 removed outlier: 4.158A pdb=" N PHE 1 170 " --> pdb=" O TRP 1 167 " (cutoff:3.500A) Processing helix chain '1' and resid 195 through 198 removed outlier: 3.846A pdb=" N LEU 1 198 " --> pdb=" O GLY 1 195 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 195 through 198' Processing helix chain '1' and resid 199 through 206 Processing helix chain '1' and resid 246 through 251 Processing helix chain '1' and resid 448 through 454 Processing helix chain '1' and resid 544 through 548 Processing helix chain '1' and resid 588 through 598 removed outlier: 3.599A pdb=" N LEU 1 597 " --> pdb=" O ARG 1 593 " (cutoff:3.500A) Processing helix chain '2' and resid 99 through 103 Processing helix chain '2' and resid 202 through 206 removed outlier: 3.875A pdb=" N THR 2 206 " --> pdb=" O ALA 2 203 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 103 Processing helix chain '4' and resid 82 through 84 No H-bonds generated for 'chain '4' and resid 82 through 84' Processing helix chain '4' and resid 99 through 103 Processing helix chain '5' and resid 99 through 103 Processing helix chain '5' and resid 202 through 206 Processing helix chain '6' and resid 20 through 27 Processing helix chain '6' and resid 30 through 52 removed outlier: 3.662A pdb=" N LEU 6 46 " --> pdb=" O ASP 6 42 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN 6 49 " --> pdb=" O ALA 6 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU 6 51 " --> pdb=" O ASN 6 47 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 75 removed outlier: 3.777A pdb=" N LEU 6 57 " --> pdb=" O PHE 6 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU 6 58 " --> pdb=" O ASN 6 54 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL 6 61 " --> pdb=" O LEU 6 57 " (cutoff:3.500A) Proline residue: 6 64 - end of helix removed outlier: 4.191A pdb=" N ALA 6 73 " --> pdb=" O ARG 6 69 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA 6 74 " --> pdb=" O LEU 6 70 " (cutoff:3.500A) Processing helix chain '6' and resid 87 through 94 removed outlier: 5.166A pdb=" N GLN 6 92 " --> pdb=" O TYR 6 89 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN 6 94 " --> pdb=" O ASP 6 91 " (cutoff:3.500A) Processing helix chain '7' and resid 19 through 62 removed outlier: 3.844A pdb=" N ASP 7 24 " --> pdb=" O GLN 7 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA 7 26 " --> pdb=" O GLU 7 22 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU 7 28 " --> pdb=" O ASP 7 24 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY 7 29 " --> pdb=" O LYS 7 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU 7 36 " --> pdb=" O ARG 7 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS 7 37 " --> pdb=" O GLU 7 33 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP 7 42 " --> pdb=" O ARG 7 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN 7 47 " --> pdb=" O HIS 7 43 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN 7 48 " --> pdb=" O GLN 7 44 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL 7 50 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS 7 55 " --> pdb=" O GLU 7 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 7 57 " --> pdb=" O PHE 7 53 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU 7 58 " --> pdb=" O ASN 7 54 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG 7 60 " --> pdb=" O ILE 7 56 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) Processing helix chain '7' and resid 64 through 72 removed outlier: 3.983A pdb=" N LEU 7 70 " --> pdb=" O GLN 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 90 through 105 removed outlier: 3.598A pdb=" N LEU 7 103 " --> pdb=" O SER 7 99 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE 7 104 " --> pdb=" O TYR 7 100 " (cutoff:3.500A) Processing helix chain '8' and resid 21 through 27 Processing helix chain '8' and resid 30 through 60 removed outlier: 3.754A pdb=" N LYS 8 37 " --> pdb=" O GLU 8 33 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN 8 44 " --> pdb=" O LYS 8 40 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN 8 49 " --> pdb=" O ALA 8 45 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU 8 51 " --> pdb=" O ASN 8 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE 8 56 " --> pdb=" O GLN 8 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU 8 57 " --> pdb=" O PHE 8 53 " (cutoff:3.500A) Processing helix chain '8' and resid 63 through 75 removed outlier: 3.921A pdb=" N ALA 8 74 " --> pdb=" O LEU 8 70 " (cutoff:3.500A) Processing helix chain '8' and resid 87 through 91 Processing helix chain '9' and resid 19 through 23 Processing helix chain '9' and resid 25 through 62 removed outlier: 3.814A pdb=" N ALA 9 35 " --> pdb=" O GLN 9 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG 9 38 " --> pdb=" O LEU 9 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU 9 46 " --> pdb=" O ASP 9 42 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS 9 55 " --> pdb=" O GLU 9 51 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE 9 56 " --> pdb=" O GLN 9 52 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN 9 59 " --> pdb=" O LYS 9 55 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 9 60 " --> pdb=" O ILE 9 56 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL 9 61 " --> pdb=" O LEU 9 57 " (cutoff:3.500A) Processing helix chain '9' and resid 63 through 72 Processing helix chain '9' and resid 89 through 105 removed outlier: 3.558A pdb=" N PHE 9 104 " --> pdb=" O TYR 9 100 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 1845 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: 42.92 Time building geometry restraints manager: 106.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 74211 1.02 - 1.22: 39 1.22 - 1.41: 32548 1.41 - 1.61: 44954 1.61 - 1.81: 444 Bond restraints: 152196 Sorted by residual: bond pdb=" N ALA H 29 " pdb=" H1 ALA H 29 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ALA R 29 " pdb=" H1 ALA R 29 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ALA T 29 " pdb=" H1 ALA T 29 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ALA 5 29 " pdb=" H1 ALA 5 29 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ALA F 29 " pdb=" H1 ALA F 29 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 152191 not shown) Histogram of bond angle deviations from ideal: 94.49 - 102.55: 290 102.55 - 110.60: 150196 110.60 - 118.65: 56125 118.65 - 126.70: 66685 126.70 - 134.76: 1339 Bond angle restraints: 274635 Sorted by residual: angle pdb=" C PHE A 642 " pdb=" N PRO A 643 " pdb=" CA PRO A 643 " ideal model delta sigma weight residual 119.84 112.24 7.60 1.25e+00 6.40e-01 3.70e+01 angle pdb=" C PHE M 642 " pdb=" N PRO M 643 " pdb=" CA PRO M 643 " ideal model delta sigma weight residual 119.84 112.25 7.59 1.25e+00 6.40e-01 3.68e+01 angle pdb=" C PHE Y 642 " pdb=" N PRO Y 643 " pdb=" CA PRO Y 643 " ideal model delta sigma weight residual 119.84 112.28 7.56 1.25e+00 6.40e-01 3.66e+01 angle pdb=" C PHE O 642 " pdb=" N PRO O 643 " pdb=" CA PRO O 643 " ideal model delta sigma weight residual 119.84 112.55 7.29 1.25e+00 6.40e-01 3.40e+01 angle pdb=" C PHE C 642 " pdb=" N PRO C 643 " pdb=" CA PRO C 643 " ideal model delta sigma weight residual 119.84 112.56 7.28 1.25e+00 6.40e-01 3.39e+01 ... (remaining 274630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 65601 16.16 - 32.32: 5321 32.32 - 48.48: 1272 48.48 - 64.63: 421 64.63 - 80.79: 45 Dihedral angle restraints: 72660 sinusoidal: 39189 harmonic: 33471 Sorted by residual: dihedral pdb=" CA ILE Y 446 " pdb=" C ILE Y 446 " pdb=" N THR Y 447 " pdb=" CA THR Y 447 " ideal model delta harmonic sigma weight residual -180.00 -141.10 -38.90 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA ILE A 446 " pdb=" C ILE A 446 " pdb=" N THR A 447 " pdb=" CA THR A 447 " ideal model delta harmonic sigma weight residual -180.00 -141.17 -38.83 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA ILE M 446 " pdb=" C ILE M 446 " pdb=" N THR M 447 " pdb=" CA THR M 447 " ideal model delta harmonic sigma weight residual 180.00 -141.19 -38.81 0 5.00e+00 4.00e-02 6.02e+01 ... (remaining 72657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 8730 0.061 - 0.123: 2679 0.123 - 0.184: 400 0.184 - 0.246: 8 0.246 - 0.307: 6 Chirality restraints: 11823 Sorted by residual: chirality pdb=" CB ILE N 541 " pdb=" CA ILE N 541 " pdb=" CG1 ILE N 541 " pdb=" CG2 ILE N 541 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE B 541 " pdb=" CA ILE B 541 " pdb=" CG1 ILE B 541 " pdb=" CG2 ILE B 541 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE Z 541 " pdb=" CA ILE Z 541 " pdb=" CG1 ILE Z 541 " pdb=" CG2 ILE Z 541 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 11820 not shown) Planarity restraints: 22992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 438 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE B 438 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE B 438 " -0.021 2.00e-02 2.50e+03 pdb=" N THR B 439 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE N 438 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE N 438 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE N 438 " -0.021 2.00e-02 2.50e+03 pdb=" N THR N 439 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Z 438 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ILE Z 438 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE Z 438 " 0.021 2.00e-02 2.50e+03 pdb=" N THR Z 439 " 0.019 2.00e-02 2.50e+03 ... (remaining 22989 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.45: 84 1.45 - 2.37: 67249 2.37 - 3.29: 591456 3.29 - 4.22: 893016 4.22 - 5.14: 1611679 Warning: very small nonbonded interaction distances. Nonbonded interactions: 3163484 Sorted by model distance: nonbonded pdb="HH21 ARG B 260 " pdb=" HB3 SER P 225 " model vdw 0.527 2.270 nonbonded pdb=" HB3 SER D 225 " pdb="HH21 ARG Z 260 " model vdw 0.527 2.270 nonbonded pdb="HH21 ARG N 260 " pdb=" HB3 SER 1 225 " model vdw 0.527 2.270 nonbonded pdb=" CD1 ILE U 21 " pdb="HE21 GLN 9 19 " model vdw 0.625 2.750 nonbonded pdb=" CD1 ILE I 21 " pdb="HE21 GLN X 19 " model vdw 0.625 2.750 ... (remaining 3163479 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 '0' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 649 or (resid 650 and (name \ N or name CA or name C or name O or name HA2 or name HA3)) or resid 651 through \ 663 or resid 701)) selection = (chain '1' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 615 or (resid 616 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 o \ r name H or name HA or name HB2 or name HB3)) or resid 617 through 649 or (resid \ 650 and (name N or name CA or name C or name O or name HA2 or name HA3)) or res \ id 651 through 663 or resid 701)) selection = (chain 'A' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 615 or (resid 616 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 o \ r name H or name HA or name HB2 or name HB3)) or resid 617 through 649 or (resid \ 650 and (name N or name CA or name C or name O or name HA2 or name HA3)) or res \ id 651 through 663 or resid 701)) selection = (chain 'B' and (resid 134 through 615 or (resid 616 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3)) or resid 617 through 663 or resid 701)) selection = (chain 'C' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 649 or (resid 650 and (name \ N or name CA or name C or name O or name HA2 or name HA3)) or resid 651 through \ 663 or resid 701)) selection = (chain 'D' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 615 or (resid 616 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 o \ r name H or name HA or name HB2 or name HB3)) or resid 617 through 649 or (resid \ 650 and (name N or name CA or name C or name O or name HA2 or name HA3)) or res \ id 651 through 663 or resid 701)) selection = (chain 'M' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 615 or (resid 616 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 o \ r name H or name HA or name HB2 or name HB3)) or resid 617 through 649 or (resid \ 650 and (name N or name CA or name C or name O or name HA2 or name HA3)) or res \ id 651 through 663 or resid 701)) selection = (chain 'N' and (resid 134 through 615 or (resid 616 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3)) or resid 617 through 663 or resid 701)) selection = (chain 'O' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 649 or (resid 650 and (name \ N or name CA or name C or name O or name HA2 or name HA3)) or resid 651 through \ 663 or resid 701)) selection = (chain 'P' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 615 or (resid 616 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 o \ r name H or name HA or name HB2 or name HB3)) or resid 617 through 649 or (resid \ 650 and (name N or name CA or name C or name O or name HA2 or name HA3)) or res \ id 651 through 663 or resid 701)) selection = (chain 'Y' and (resid 134 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 403 through 430 or (r \ esid 431 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA )) or resid 432 through 615 or (resid 616 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 o \ r name H or name HA or name HB2 or name HB3)) or resid 617 through 649 or (resid \ 650 and (name N or name CA or name C or name O or name HA2 or name HA3)) or res \ id 651 through 663 or resid 701)) selection = (chain 'Z' and (resid 134 through 615 or (resid 616 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3)) or resid 617 through 663 or resid 701)) } ncs_group { reference = (chain '2' and resid 30 through 228) selection = (chain '3' and resid 30 through 228) selection = (chain '4' and resid 30 through 228) selection = (chain '5' and resid 30 through 228) selection = (chain 'E' and resid 30 through 228) selection = (chain 'F' and resid 30 through 228) selection = (chain 'G' and resid 30 through 228) selection = (chain 'H' and resid 30 through 228) selection = (chain 'Q' and resid 30 through 228) selection = (chain 'R' and resid 30 through 228) selection = (chain 'S' and resid 30 through 228) selection = (chain 'T' and resid 30 through 228) } ncs_group { reference = (chain '6' and (resid 19 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H o \ r name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or resi \ d 87 through 100)) selection = (chain '7' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 20 through 86 or ( \ resid 87 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA )) or resid 88 through 100)) selection = (chain '8' and (resid 19 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H o \ r name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or resi \ d 87 through 100)) selection = (chain '9' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 20 through 85 or ( \ resid 86 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HE21)) or (resid 87 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA )) o \ r resid 88 through 100)) selection = (chain 'I' and (resid 19 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H o \ r name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or resi \ d 87 through 100)) selection = (chain 'J' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 20 through 86 or ( \ resid 87 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA )) or resid 88 through 100)) selection = (chain 'K' and (resid 19 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H o \ r name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or resi \ d 87 through 100)) selection = (chain 'L' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 20 through 85 or ( \ resid 86 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HE21)) or (resid 87 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA )) o \ r resid 88 through 100)) selection = (chain 'U' and (resid 19 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H o \ r name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or resi \ d 87 through 100)) selection = (chain 'V' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 20 through 86 or ( \ resid 87 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA )) or resid 88 through 100)) selection = (chain 'W' and (resid 19 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H o \ r name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or resi \ d 87 through 100)) selection = (chain 'X' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 20 through 85 or ( \ resid 86 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HE21)) or (resid 87 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA )) o \ r resid 88 through 100)) } 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: 0.010 Normalize map: mean=0, sd=1: 22.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.780 Extract box with map and model: 46.810 Check model and map are aligned: 1.660 Set scattering table: 1.040 Process input model: 371.580 Find NCS groups from input model: 8.340 Set up NCS constraints: 0.690 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: 0.030 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 457.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 0.110 77949 Z= 0.709 Angle : 0.920 9.782 106047 Z= 0.500 Chirality : 0.056 0.307 11823 Planarity : 0.006 0.066 13761 Dihedral : 9.919 80.793 28224 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.28 % Favored : 84.54 % Rotamer: Outliers : 0.71 % Allowed : 2.60 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.00 (0.07), residues: 9759 helix: -3.63 (0.09), residues: 1233 sheet: -3.39 (0.09), residues: 2406 loop : -3.37 (0.07), residues: 6120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 1 179 HIS 0.013 0.003 HIS 1 355 PHE 0.027 0.003 PHE P 607 TYR 0.023 0.003 TYR Y 468 ARG 0.011 0.001 ARG Y 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 2119 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 2059 time to evaluate : 8.982 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 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 172 SER cc_start: 0.8836 (m) cc_final: 0.8508 (p) REVERT: A 372 ASN cc_start: 0.8383 (t0) cc_final: 0.8148 (t0) REVERT: B 151 MET cc_start: 0.7882 (mmm) cc_final: 0.7386 (tpp) REVERT: B 182 SER cc_start: 0.9516 (m) cc_final: 0.8554 (t) REVERT: B 277 TYR cc_start: 0.8811 (p90) cc_final: 0.8285 (p90) REVERT: B 332 MET cc_start: 0.6637 (mmt) cc_final: 0.6293 (mtt) REVERT: B 345 LYS cc_start: 0.8910 (mttp) cc_final: 0.8605 (mtmt) REVERT: B 499 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8255 (mm-30) REVERT: B 544 ASP cc_start: 0.7832 (m-30) cc_final: 0.7548 (m-30) REVERT: B 641 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6584 (mm-30) REVERT: B 657 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7838 (mtt-85) REVERT: B 660 SER cc_start: 0.8448 (p) cc_final: 0.8068 (t) REVERT: C 156 ASP cc_start: 0.8399 (m-30) cc_final: 0.8121 (m-30) REVERT: C 271 ASP cc_start: 0.8527 (t0) cc_final: 0.7763 (p0) REVERT: C 297 ILE cc_start: 0.8644 (mt) cc_final: 0.8332 (mm) REVERT: C 498 ILE cc_start: 0.9349 (pt) cc_final: 0.8887 (pt) REVERT: D 182 SER cc_start: 0.8989 (m) cc_final: 0.8595 (t) REVERT: D 523 THR cc_start: 0.8329 (m) cc_final: 0.7925 (p) REVERT: F 133 LYS cc_start: 0.8750 (tttt) cc_final: 0.8472 (tmtt) REVERT: F 175 GLU cc_start: 0.9005 (pm20) cc_final: 0.8392 (pm20) REVERT: G 196 LEU cc_start: 0.8318 (tp) cc_final: 0.7929 (tp) REVERT: H 56 ASN cc_start: 0.8670 (t0) cc_final: 0.8436 (t0) REVERT: H 128 LEU cc_start: 0.9333 (mt) cc_final: 0.9128 (mm) REVERT: I 23 LEU cc_start: 0.6973 (pp) cc_final: 0.6717 (mt) REVERT: I 24 ASP cc_start: 0.7631 (t0) cc_final: 0.7352 (t0) REVERT: I 62 GLN cc_start: 0.8562 (tp40) cc_final: 0.8166 (tp40) REVERT: J 21 ILE cc_start: 0.6764 (mt) cc_final: 0.6492 (mt) REVERT: J 46 LEU cc_start: 0.8828 (tp) cc_final: 0.8613 (tt) REVERT: J 50 VAL cc_start: 0.8997 (t) cc_final: 0.8001 (t) REVERT: J 55 LYS cc_start: 0.8348 (pttp) cc_final: 0.7694 (pttt) REVERT: K 42 ASP cc_start: 0.8523 (m-30) cc_final: 0.7838 (t70) REVERT: K 54 ASN cc_start: 0.8712 (t0) cc_final: 0.8439 (t0) REVERT: K 85 ASP cc_start: 0.7229 (t70) cc_final: 0.6958 (t70) REVERT: K 90 ASP cc_start: 0.8995 (m-30) cc_final: 0.8332 (p0) REVERT: L 21 ILE cc_start: 0.7168 (mt) cc_final: 0.6713 (mm) REVERT: L 81 TYR cc_start: 0.8316 (m-10) cc_final: 0.7904 (m-80) REVERT: N 277 TYR cc_start: 0.8728 (p90) cc_final: 0.8383 (p90) REVERT: N 300 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7963 (p90) REVERT: N 345 LYS cc_start: 0.8857 (mttp) cc_final: 0.8353 (mtpp) REVERT: N 408 VAL cc_start: 0.9327 (m) cc_final: 0.9123 (p) REVERT: N 423 ASP cc_start: 0.8699 (p0) cc_final: 0.8065 (p0) REVERT: N 499 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8254 (mm-30) REVERT: N 641 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: N 660 SER cc_start: 0.8628 (p) cc_final: 0.8357 (t) REVERT: O 156 ASP cc_start: 0.8404 (m-30) cc_final: 0.8160 (m-30) REVERT: O 242 ASP cc_start: 0.8112 (t0) cc_final: 0.7879 (m-30) REVERT: O 322 LYS cc_start: 0.8860 (mttp) cc_final: 0.8658 (mtpp) REVERT: O 556 GLU cc_start: 0.8223 (tt0) cc_final: 0.7925 (tt0) REVERT: P 168 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7969 (mt-10) REVERT: P 182 SER cc_start: 0.9094 (m) cc_final: 0.8636 (t) REVERT: P 267 PHE cc_start: 0.8904 (m-80) cc_final: 0.8681 (m-80) REVERT: P 605 ASP cc_start: 0.8300 (p0) cc_final: 0.8035 (p0) REVERT: Q 38 ARG cc_start: 0.8429 (mmt90) cc_final: 0.8214 (mmt90) REVERT: Q 156 ASP cc_start: 0.7547 (m-30) cc_final: 0.7138 (m-30) REVERT: Q 164 TYR cc_start: 0.7204 (m-80) cc_final: 0.6989 (m-10) REVERT: R 179 ASN cc_start: 0.8001 (t0) cc_final: 0.7770 (t0) REVERT: R 221 MET cc_start: 0.8685 (mmm) cc_final: 0.8280 (tpp) REVERT: S 196 LEU cc_start: 0.8139 (tp) cc_final: 0.7769 (tp) REVERT: T 38 ARG cc_start: 0.8351 (mmt90) cc_final: 0.8072 (mmt90) REVERT: T 179 ASN cc_start: 0.7567 (t0) cc_final: 0.7346 (t0) REVERT: U 23 LEU cc_start: 0.6882 (pp) cc_final: 0.6442 (mt) REVERT: U 24 ASP cc_start: 0.7459 (t0) cc_final: 0.7143 (t0) REVERT: V 34 LEU cc_start: 0.8135 (mt) cc_final: 0.7790 (mt) REVERT: V 72 ARG cc_start: 0.8782 (ttm170) cc_final: 0.8230 (mtp85) REVERT: W 42 ASP cc_start: 0.8341 (m-30) cc_final: 0.7947 (t70) REVERT: W 62 GLN cc_start: 0.8513 (tp40) cc_final: 0.8237 (mm-40) REVERT: W 66 GLN cc_start: 0.8720 (tt0) cc_final: 0.8517 (mt0) REVERT: W 90 ASP cc_start: 0.8928 (m-30) cc_final: 0.8370 (p0) REVERT: X 21 ILE cc_start: 0.7308 (mt) cc_final: 0.7068 (mm) REVERT: X 38 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8353 (mtp85) REVERT: X 42 ASP cc_start: 0.8955 (m-30) cc_final: 0.8545 (m-30) REVERT: X 88 PHE cc_start: 0.6785 (t80) cc_final: 0.6478 (t80) REVERT: Y 487 PHE cc_start: 0.8720 (m-80) cc_final: 0.8436 (m-10) REVERT: Y 610 TYR cc_start: 0.8507 (m-80) cc_final: 0.8119 (m-80) REVERT: Z 182 SER cc_start: 0.9519 (m) cc_final: 0.8413 (t) REVERT: Z 277 TYR cc_start: 0.8772 (p90) cc_final: 0.8235 (p90) REVERT: Z 300 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.8057 (p90) REVERT: Z 380 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7881 (mm-30) REVERT: Z 499 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8543 (mt-10) REVERT: Z 598 ASN cc_start: 0.8791 (m-40) cc_final: 0.8543 (m110) REVERT: Z 641 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: 0 182 SER cc_start: 0.9349 (m) cc_final: 0.9064 (p) REVERT: 0 209 TYR cc_start: 0.7230 (m-10) cc_final: 0.7029 (m-80) REVERT: 0 242 ASP cc_start: 0.8168 (t0) cc_final: 0.7913 (m-30) REVERT: 0 582 ASP cc_start: 0.8337 (m-30) cc_final: 0.8094 (m-30) REVERT: 1 362 PHE cc_start: 0.8913 (m-80) cc_final: 0.8498 (m-80) REVERT: 1 447 THR cc_start: 0.8572 (p) cc_final: 0.8311 (t) REVERT: 1 523 THR cc_start: 0.8269 (m) cc_final: 0.7917 (p) REVERT: 1 642 PHE cc_start: 0.8014 (t80) cc_final: 0.7742 (t80) REVERT: 2 156 ASP cc_start: 0.7408 (m-30) cc_final: 0.7021 (m-30) REVERT: 3 167 LYS cc_start: 0.8405 (tttt) cc_final: 0.8173 (tttt) REVERT: 3 175 GLU cc_start: 0.8904 (pm20) cc_final: 0.8542 (pm20) REVERT: 4 177 LYS cc_start: 0.8383 (mptp) cc_final: 0.8136 (mmtm) REVERT: 5 38 ARG cc_start: 0.8580 (mmt90) cc_final: 0.8369 (mmt-90) REVERT: 5 56 ASN cc_start: 0.8642 (t0) cc_final: 0.8402 (t0) REVERT: 5 174 LEU cc_start: 0.8767 (tm) cc_final: 0.8409 (tm) REVERT: 5 179 ASN cc_start: 0.7342 (t0) cc_final: 0.7048 (t0) REVERT: 6 19 GLN cc_start: 0.7218 (mt0) cc_final: 0.6897 (pm20) REVERT: 6 23 LEU cc_start: 0.6681 (pp) cc_final: 0.6289 (mt) REVERT: 6 24 ASP cc_start: 0.7414 (t0) cc_final: 0.7111 (t0) REVERT: 8 42 ASP cc_start: 0.8381 (m-30) cc_final: 0.7847 (t70) REVERT: 8 54 ASN cc_start: 0.8746 (t0) cc_final: 0.8540 (t0) REVERT: 8 90 ASP cc_start: 0.8982 (m-30) cc_final: 0.8529 (p0) outliers start: 60 outliers final: 45 residues processed: 2109 average time/residue: 2.1470 time to fit residues: 7231.4873 Evaluate side-chains 1136 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1086 time to evaluate : 9.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 300 TYR Chi-restraints excluded: chain D residue 516 HIS Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 641 GLU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain N residue 641 GLU Chi-restraints excluded: chain N residue 644 LEU Chi-restraints excluded: chain N residue 645 THR Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 218 VAL Chi-restraints excluded: chain P residue 300 TYR Chi-restraints excluded: chain P residue 516 HIS Chi-restraints excluded: chain P residue 627 ASP Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 87 ASN Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 641 GLU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 216 ILE Chi-restraints excluded: chain 1 residue 218 VAL Chi-restraints excluded: chain 1 residue 300 TYR Chi-restraints excluded: chain 1 residue 516 HIS Chi-restraints excluded: chain 1 residue 627 ASP Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 8 residue 87 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 3.9990 chunk 736 optimal weight: 0.9980 chunk 408 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 496 optimal weight: 5.9990 chunk 393 optimal weight: 4.9990 chunk 761 optimal weight: 0.6980 chunk 294 optimal weight: 10.0000 chunk 463 optimal weight: 7.9990 chunk 567 optimal weight: 8.9990 chunk 882 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN H 90 HIS ** H 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN I 86 GLN J 44 GLN J 49 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN L 19 GLN L 86 GLN L 94 ASN ** M 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 245 GLN ** N 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 513 GLN P 378 ASN ** R 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 190 ASN T 90 HIS ** T 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN U 86 GLN V 43 HIS ** V 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS W 48 ASN X 19 GLN X 86 GLN ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 192 GLN ** Z 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 190 ASN 5 90 HIS ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 31 GLN 6 44 GLN 6 86 GLN 7 43 HIS 7 49 GLN 7 66 GLN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 48 ASN 9 19 GLN 9 44 GLN 9 86 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 77949 Z= 0.267 Angle : 0.673 8.333 106047 Z= 0.355 Chirality : 0.045 0.202 11823 Planarity : 0.006 0.086 13761 Dihedral : 7.388 49.180 10708 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.71 % Favored : 88.16 % Rotamer: Outliers : 1.93 % Allowed : 7.94 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.37 (0.07), residues: 9759 helix: -2.57 (0.12), residues: 1230 sheet: -3.13 (0.09), residues: 2448 loop : -2.99 (0.07), residues: 6081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 4 204 HIS 0.009 0.001 HIS W 43 PHE 0.028 0.001 PHE Y 642 TYR 0.015 0.001 TYR M 533 ARG 0.014 0.001 ARG 6 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1354 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1191 time to evaluate : 8.980 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 372 ASN cc_start: 0.8424 (t0) cc_final: 0.8221 (t0) REVERT: A 380 GLU cc_start: 0.8479 (tt0) cc_final: 0.8208 (tt0) REVERT: A 467 MET cc_start: 0.8215 (mtt) cc_final: 0.7504 (mtt) REVERT: B 151 MET cc_start: 0.7980 (mmm) cc_final: 0.7688 (tpp) REVERT: B 271 ASP cc_start: 0.8565 (t0) cc_final: 0.8246 (t0) REVERT: B 277 TYR cc_start: 0.8819 (p90) cc_final: 0.8432 (p90) REVERT: B 332 MET cc_start: 0.6120 (mmt) cc_final: 0.5902 (mtt) REVERT: B 345 LYS cc_start: 0.8949 (mttp) cc_final: 0.8665 (mtmt) REVERT: B 351 ILE cc_start: 0.8988 (pt) cc_final: 0.8580 (mt) REVERT: B 499 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8776 (mt-10) REVERT: B 544 ASP cc_start: 0.7976 (m-30) cc_final: 0.7742 (m-30) REVERT: B 657 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7984 (mtt-85) REVERT: C 271 ASP cc_start: 0.8487 (t0) cc_final: 0.7621 (p0) REVERT: C 297 ILE cc_start: 0.8646 (mt) cc_final: 0.8382 (mm) REVERT: C 351 ILE cc_start: 0.9105 (pt) cc_final: 0.8839 (mt) REVERT: D 523 THR cc_start: 0.8377 (m) cc_final: 0.8021 (p) REVERT: F 56 ASN cc_start: 0.8581 (t0) cc_final: 0.8344 (p0) REVERT: F 124 GLN cc_start: 0.6570 (tm-30) cc_final: 0.6361 (tm-30) REVERT: F 133 LYS cc_start: 0.9055 (tttt) cc_final: 0.8480 (tmtt) REVERT: H 56 ASN cc_start: 0.8648 (t0) cc_final: 0.8430 (t0) REVERT: H 128 LEU cc_start: 0.9349 (mt) cc_final: 0.9135 (mm) REVERT: I 58 GLU cc_start: 0.7919 (tp30) cc_final: 0.7550 (tp30) REVERT: J 66 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8472 (mm110) REVERT: K 42 ASP cc_start: 0.8520 (m-30) cc_final: 0.7981 (t70) REVERT: K 54 ASN cc_start: 0.8418 (t0) cc_final: 0.8121 (t0) REVERT: K 85 ASP cc_start: 0.7934 (t70) cc_final: 0.7566 (t70) REVERT: K 86 GLN cc_start: 0.8708 (tp40) cc_final: 0.8485 (tp40) REVERT: K 90 ASP cc_start: 0.8995 (m-30) cc_final: 0.8352 (p0) REVERT: L 93 LEU cc_start: 0.8857 (tt) cc_final: 0.8600 (mt) REVERT: M 284 ASP cc_start: 0.8450 (p0) cc_final: 0.8160 (p0) REVERT: M 467 MET cc_start: 0.8166 (mtt) cc_final: 0.7949 (mtt) REVERT: N 277 TYR cc_start: 0.8772 (p90) cc_final: 0.8453 (p90) REVERT: N 280 MET cc_start: 0.8818 (mmt) cc_final: 0.8581 (mmt) REVERT: N 300 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7960 (p90) REVERT: N 345 LYS cc_start: 0.8926 (mttp) cc_final: 0.8341 (mtpp) REVERT: N 380 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7721 (mt-10) REVERT: N 408 VAL cc_start: 0.9348 (m) cc_final: 0.9134 (p) REVERT: N 423 ASP cc_start: 0.8784 (p0) cc_final: 0.8026 (p0) REVERT: N 499 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8691 (mt-10) REVERT: O 242 ASP cc_start: 0.8208 (t0) cc_final: 0.7935 (m-30) REVERT: P 157 MET cc_start: 0.7862 (ttp) cc_final: 0.7476 (ttp) REVERT: P 168 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8096 (mt-10) REVERT: P 523 THR cc_start: 0.8618 (m) cc_final: 0.8206 (p) REVERT: P 605 ASP cc_start: 0.8472 (p0) cc_final: 0.8148 (p0) REVERT: P 629 PHE cc_start: 0.8393 (m-80) cc_final: 0.8113 (m-80) REVERT: R 156 ASP cc_start: 0.8466 (m-30) cc_final: 0.8024 (m-30) REVERT: R 179 ASN cc_start: 0.7983 (t0) cc_final: 0.7756 (t0) REVERT: T 124 GLN cc_start: 0.8655 (tt0) cc_final: 0.8240 (tp40) REVERT: U 23 LEU cc_start: 0.7067 (pp) cc_final: 0.6712 (mt) REVERT: V 58 GLU cc_start: 0.8584 (mp0) cc_final: 0.8213 (mp0) REVERT: V 66 GLN cc_start: 0.8473 (tp40) cc_final: 0.8255 (mm110) REVERT: W 42 ASP cc_start: 0.8470 (m-30) cc_final: 0.8133 (t70) REVERT: W 66 GLN cc_start: 0.8727 (tt0) cc_final: 0.8499 (mt0) REVERT: W 86 GLN cc_start: 0.8741 (tp40) cc_final: 0.8460 (tp40) REVERT: W 90 ASP cc_start: 0.9045 (m-30) cc_final: 0.8417 (p0) REVERT: Y 284 ASP cc_start: 0.8329 (p0) cc_final: 0.7925 (p0) REVERT: Y 372 ASN cc_start: 0.7856 (t0) cc_final: 0.7636 (t0) REVERT: Y 487 PHE cc_start: 0.8738 (m-80) cc_final: 0.8351 (m-80) REVERT: Z 277 TYR cc_start: 0.8800 (p90) cc_final: 0.8452 (p90) REVERT: Z 300 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7883 (p90) REVERT: Z 351 ILE cc_start: 0.9048 (pt) cc_final: 0.8533 (mt) REVERT: Z 499 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8537 (mt-10) REVERT: 0 182 SER cc_start: 0.9329 (m) cc_final: 0.9067 (p) REVERT: 0 242 ASP cc_start: 0.8355 (t0) cc_final: 0.7989 (m-30) REVERT: 0 351 ILE cc_start: 0.9050 (pt) cc_final: 0.8693 (mt) REVERT: 1 447 THR cc_start: 0.8553 (p) cc_final: 0.8242 (t) REVERT: 1 523 THR cc_start: 0.8304 (m) cc_final: 0.7981 (p) REVERT: 2 74 TYR cc_start: 0.8970 (t80) cc_final: 0.8608 (t80) REVERT: 4 177 LYS cc_start: 0.8015 (mptp) cc_final: 0.7654 (mptt) REVERT: 5 172 MET cc_start: 0.8237 (mmm) cc_final: 0.7867 (mmm) REVERT: 5 179 ASN cc_start: 0.7228 (t0) cc_final: 0.6959 (t0) REVERT: 6 19 GLN cc_start: 0.6907 (mt0) cc_final: 0.6616 (pm20) REVERT: 8 42 ASP cc_start: 0.8461 (m-30) cc_final: 0.7999 (t70) REVERT: 8 82 SER cc_start: 0.9396 (m) cc_final: 0.9049 (p) REVERT: 8 90 ASP cc_start: 0.9034 (m-30) cc_final: 0.8580 (p0) REVERT: 9 52 GLN cc_start: 0.8092 (tp40) cc_final: 0.7746 (tt0) outliers start: 163 outliers final: 129 residues processed: 1314 average time/residue: 1.9689 time to fit residues: 4244.5042 Evaluate side-chains 1152 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1021 time to evaluate : 8.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 361 ASP Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 627 ASP Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 641 GLU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain N residue 644 LEU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 337 SER Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 489 THR Chi-restraints excluded: chain O residue 591 THR Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 183 GLU Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 218 VAL Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 380 GLU Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain P residue 544 ASP Chi-restraints excluded: chain P residue 627 ASP Chi-restraints excluded: chain Q residue 172 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 168 ASP Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 137 HIS Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain V residue 87 ASN Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 641 GLU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 157 MET Chi-restraints excluded: chain 0 residue 345 LYS Chi-restraints excluded: chain 0 residue 591 THR Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 167 TRP Chi-restraints excluded: chain 1 residue 216 ILE Chi-restraints excluded: chain 1 residue 282 ASP Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 544 ASP Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 1 residue 627 ASP Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 3 residue 116 ASN Chi-restraints excluded: chain 3 residue 138 ILE Chi-restraints excluded: chain 4 residue 76 ASN Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 5 residue 42 ASP Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 82 SER Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 8 residue 48 ASN Chi-restraints excluded: chain 9 residue 54 ASN Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 3.9990 chunk 273 optimal weight: 0.0870 chunk 734 optimal weight: 2.9990 chunk 601 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 884 optimal weight: 7.9990 chunk 955 optimal weight: 0.9990 chunk 787 optimal weight: 7.9990 chunk 876 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 709 optimal weight: 6.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN ** M 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN ** N 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN V 43 HIS ** V 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 86 GLN ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 379 GLN Y 474 GLN Z 178 ASN Z 192 GLN ** Z 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 86 GLN 9 94 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 77949 Z= 0.225 Angle : 0.604 7.129 106047 Z= 0.315 Chirality : 0.044 0.181 11823 Planarity : 0.005 0.069 13761 Dihedral : 6.615 47.189 10676 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.36 % Favored : 88.51 % Rotamer: Outliers : 1.88 % Allowed : 9.18 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.89 (0.08), residues: 9759 helix: -1.99 (0.13), residues: 1215 sheet: -2.83 (0.09), residues: 2475 loop : -2.70 (0.08), residues: 6069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.008 0.001 HIS V 43 PHE 0.023 0.001 PHE 8 88 TYR 0.024 0.001 TYR X 89 ARG 0.007 0.000 ARG 6 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1256 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1098 time to evaluate : 10.729 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 372 ASN cc_start: 0.8503 (t0) cc_final: 0.8269 (t0) REVERT: A 380 GLU cc_start: 0.8498 (tt0) cc_final: 0.8143 (tt0) REVERT: A 467 MET cc_start: 0.8638 (mtt) cc_final: 0.8007 (mtt) REVERT: B 151 MET cc_start: 0.8118 (mmm) cc_final: 0.7886 (tpp) REVERT: B 277 TYR cc_start: 0.8805 (p90) cc_final: 0.8457 (p90) REVERT: B 332 MET cc_start: 0.6160 (mmt) cc_final: 0.5872 (mtt) REVERT: B 351 ILE cc_start: 0.8925 (pt) cc_final: 0.8604 (mt) REVERT: B 499 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8762 (mt-10) REVERT: C 157 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7633 (ptt) REVERT: C 271 ASP cc_start: 0.8550 (t0) cc_final: 0.7558 (p0) REVERT: C 297 ILE cc_start: 0.8727 (mt) cc_final: 0.8464 (mm) REVERT: C 351 ILE cc_start: 0.9132 (pt) cc_final: 0.8830 (mt) REVERT: C 398 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6525 (mm-30) REVERT: D 523 THR cc_start: 0.8410 (m) cc_final: 0.8074 (p) REVERT: E 219 MET cc_start: 0.8508 (tpp) cc_final: 0.7937 (pmm) REVERT: F 56 ASN cc_start: 0.8542 (t0) cc_final: 0.8302 (p0) REVERT: H 56 ASN cc_start: 0.8632 (t0) cc_final: 0.8409 (t0) REVERT: H 128 LEU cc_start: 0.9368 (mt) cc_final: 0.9155 (mm) REVERT: H 221 MET cc_start: 0.8823 (mmm) cc_final: 0.8441 (ttm) REVERT: I 58 GLU cc_start: 0.8159 (tp30) cc_final: 0.7057 (tp30) REVERT: I 62 GLN cc_start: 0.8693 (tp40) cc_final: 0.8366 (tp40) REVERT: J 44 GLN cc_start: 0.9298 (tp40) cc_final: 0.9046 (tp40) REVERT: J 54 ASN cc_start: 0.8562 (m-40) cc_final: 0.8361 (m110) REVERT: J 66 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8579 (mm110) REVERT: K 30 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7541 (tp40) REVERT: K 42 ASP cc_start: 0.8557 (m-30) cc_final: 0.8043 (t70) REVERT: K 54 ASN cc_start: 0.8403 (t0) cc_final: 0.8063 (t0) REVERT: K 82 SER cc_start: 0.9575 (m) cc_final: 0.9273 (p) REVERT: K 85 ASP cc_start: 0.7873 (t70) cc_final: 0.7613 (t70) REVERT: K 86 GLN cc_start: 0.8696 (tp40) cc_final: 0.8468 (tp40) REVERT: K 90 ASP cc_start: 0.8896 (m-30) cc_final: 0.8349 (p0) REVERT: L 85 ASP cc_start: 0.8243 (p0) cc_final: 0.8040 (p0) REVERT: M 452 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6206 (p90) REVERT: M 499 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8035 (mt-10) REVERT: N 151 MET cc_start: 0.6445 (tpp) cc_final: 0.6154 (tpp) REVERT: N 277 TYR cc_start: 0.8798 (p90) cc_final: 0.8473 (p90) REVERT: N 280 MET cc_start: 0.8857 (mmt) cc_final: 0.8498 (mmt) REVERT: N 300 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7953 (p90) REVERT: N 345 LYS cc_start: 0.9010 (mttp) cc_final: 0.8428 (mtpp) REVERT: N 423 ASP cc_start: 0.8910 (p0) cc_final: 0.8184 (p0) REVERT: N 499 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8674 (mt-10) REVERT: O 157 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6915 (ptm) REVERT: O 351 ILE cc_start: 0.9089 (pt) cc_final: 0.8637 (mt) REVERT: O 469 ILE cc_start: 0.6891 (mp) cc_final: 0.6524 (mm) REVERT: O 641 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8031 (mt-10) REVERT: P 523 THR cc_start: 0.8662 (m) cc_final: 0.8315 (p) REVERT: P 605 ASP cc_start: 0.8534 (p0) cc_final: 0.8232 (p0) REVERT: P 629 PHE cc_start: 0.8559 (m-80) cc_final: 0.8209 (m-80) REVERT: Q 36 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7925 (p0) REVERT: R 179 ASN cc_start: 0.7861 (t0) cc_final: 0.7458 (t0) REVERT: S 90 HIS cc_start: 0.7714 (p-80) cc_final: 0.7233 (p-80) REVERT: T 124 GLN cc_start: 0.8639 (tt0) cc_final: 0.8199 (tp40) REVERT: T 172 MET cc_start: 0.8716 (mmm) cc_final: 0.8500 (mmm) REVERT: U 23 LEU cc_start: 0.7123 (pp) cc_final: 0.6742 (mt) REVERT: U 58 GLU cc_start: 0.8478 (tp30) cc_final: 0.7959 (tp30) REVERT: U 79 ASP cc_start: 0.8740 (t0) cc_final: 0.8521 (t70) REVERT: U 83 TYR cc_start: 0.9122 (p90) cc_final: 0.8860 (p90) REVERT: V 51 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8269 (tp30) REVERT: V 54 ASN cc_start: 0.9283 (m-40) cc_final: 0.8656 (m-40) REVERT: V 58 GLU cc_start: 0.8594 (mp0) cc_final: 0.8210 (mp0) REVERT: V 90 ASP cc_start: 0.8493 (m-30) cc_final: 0.8158 (m-30) REVERT: W 42 ASP cc_start: 0.8453 (m-30) cc_final: 0.8080 (t70) REVERT: W 82 SER cc_start: 0.9596 (m) cc_final: 0.9249 (p) REVERT: W 86 GLN cc_start: 0.8744 (tp40) cc_final: 0.8403 (tp40) REVERT: W 90 ASP cc_start: 0.8757 (m-30) cc_final: 0.8321 (p0) REVERT: X 40 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8870 (mmtt) REVERT: Y 372 ASN cc_start: 0.7860 (t0) cc_final: 0.7639 (t0) REVERT: Y 452 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6711 (p90) REVERT: Y 487 PHE cc_start: 0.8747 (m-80) cc_final: 0.8410 (m-80) REVERT: Y 610 TYR cc_start: 0.8684 (m-80) cc_final: 0.8394 (m-80) REVERT: Z 277 TYR cc_start: 0.8831 (p90) cc_final: 0.8531 (p90) REVERT: Z 300 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7817 (p90) REVERT: Z 351 ILE cc_start: 0.8924 (pt) cc_final: 0.8505 (mt) REVERT: Z 499 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8534 (mt-10) REVERT: 0 182 SER cc_start: 0.9379 (m) cc_final: 0.9080 (p) REVERT: 0 242 ASP cc_start: 0.8474 (t0) cc_final: 0.8099 (m-30) REVERT: 0 351 ILE cc_start: 0.9006 (pt) cc_final: 0.8638 (mt) REVERT: 1 447 THR cc_start: 0.8543 (p) cc_final: 0.8253 (t) REVERT: 1 523 THR cc_start: 0.8358 (m) cc_final: 0.8043 (p) REVERT: 2 219 MET cc_start: 0.8479 (tpp) cc_final: 0.7977 (ttp) REVERT: 3 96 HIS cc_start: 0.7917 (m170) cc_final: 0.7703 (m-70) REVERT: 4 90 HIS cc_start: 0.7594 (p-80) cc_final: 0.7155 (p-80) REVERT: 5 124 GLN cc_start: 0.7969 (tp40) cc_final: 0.7660 (tp40) REVERT: 5 172 MET cc_start: 0.8245 (mmm) cc_final: 0.7871 (mmm) REVERT: 6 69 ARG cc_start: 0.8249 (ttm170) cc_final: 0.8041 (ttm170) REVERT: 8 40 LYS cc_start: 0.8789 (tppp) cc_final: 0.8338 (tppt) REVERT: 8 42 ASP cc_start: 0.8472 (m-30) cc_final: 0.7999 (t70) REVERT: 8 82 SER cc_start: 0.9415 (m) cc_final: 0.9092 (p) REVERT: 8 90 ASP cc_start: 0.8837 (m-30) cc_final: 0.8581 (p0) outliers start: 158 outliers final: 128 residues processed: 1217 average time/residue: 1.9300 time to fit residues: 3896.0856 Evaluate side-chains 1113 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 976 time to evaluate : 8.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 361 ASP Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 641 GLU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 488 ILE Chi-restraints excluded: chain N residue 490 THR Chi-restraints excluded: chain N residue 495 ASP Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain N residue 644 LEU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 183 GLU Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 218 VAL Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain P residue 544 ASP Chi-restraints excluded: chain P residue 582 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 33 GLU Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain V residue 87 ASN Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 86 GLN Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 641 GLU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 345 LYS Chi-restraints excluded: chain 0 residue 489 THR Chi-restraints excluded: chain 0 residue 591 THR Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 167 TRP Chi-restraints excluded: chain 1 residue 216 ILE Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 351 ILE Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 4 residue 33 SER Chi-restraints excluded: chain 4 residue 76 ASN Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 4 residue 180 ARG Chi-restraints excluded: chain 5 residue 42 ASP Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 86 GLN Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 10.0000 chunk 664 optimal weight: 5.9990 chunk 458 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 422 optimal weight: 0.0980 chunk 593 optimal weight: 20.0000 chunk 887 optimal weight: 10.0000 chunk 939 optimal weight: 6.9990 chunk 463 optimal weight: 9.9990 chunk 841 optimal weight: 10.0000 chunk 253 optimal weight: 0.0050 overall best weight: 3.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN ** M 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 474 GLN ** N 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 463 ASN ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 HIS ** V 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN ** Y 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 474 GLN ** Z 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 86 GLN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 77949 Z= 0.253 Angle : 0.590 7.079 106047 Z= 0.307 Chirality : 0.044 0.171 11823 Planarity : 0.004 0.053 13761 Dihedral : 6.266 45.117 10672 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.48 % Favored : 88.40 % Rotamer: Outliers : 2.22 % Allowed : 9.97 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.08), residues: 9759 helix: -1.56 (0.13), residues: 1236 sheet: -2.69 (0.09), residues: 2481 loop : -2.57 (0.08), residues: 6042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 4 204 HIS 0.008 0.001 HIS V 43 PHE 0.026 0.001 PHE D 642 TYR 0.024 0.001 TYR X 89 ARG 0.007 0.000 ARG D 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1195 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1008 time to evaluate : 8.965 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 372 ASN cc_start: 0.8596 (t0) cc_final: 0.8385 (t0) REVERT: A 380 GLU cc_start: 0.8524 (tt0) cc_final: 0.8105 (tt0) REVERT: A 467 MET cc_start: 0.8864 (mtt) cc_final: 0.8259 (mtt) REVERT: B 151 MET cc_start: 0.8193 (mmm) cc_final: 0.7903 (tpp) REVERT: B 277 TYR cc_start: 0.8903 (p90) cc_final: 0.8586 (p90) REVERT: B 332 MET cc_start: 0.6066 (mmt) cc_final: 0.5705 (mtt) REVERT: B 345 LYS cc_start: 0.9210 (mmtp) cc_final: 0.8769 (mtpt) REVERT: B 351 ILE cc_start: 0.8863 (pt) cc_final: 0.8586 (mt) REVERT: C 157 MET cc_start: 0.7768 (ptm) cc_final: 0.7529 (ptt) REVERT: C 247 THR cc_start: 0.9402 (p) cc_final: 0.9034 (t) REVERT: C 297 ILE cc_start: 0.8759 (mt) cc_final: 0.8531 (mm) REVERT: C 351 ILE cc_start: 0.9106 (pt) cc_final: 0.8813 (mt) REVERT: D 523 THR cc_start: 0.8518 (m) cc_final: 0.8230 (p) REVERT: E 219 MET cc_start: 0.8492 (tpp) cc_final: 0.7956 (pmm) REVERT: F 124 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6786 (tm-30) REVERT: H 56 ASN cc_start: 0.8634 (t0) cc_final: 0.8414 (t0) REVERT: H 174 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8509 (tm) REVERT: H 221 MET cc_start: 0.8824 (mmm) cc_final: 0.8429 (ttm) REVERT: I 58 GLU cc_start: 0.8218 (tp30) cc_final: 0.7163 (tp30) REVERT: I 62 GLN cc_start: 0.8718 (tp40) cc_final: 0.8449 (tp40) REVERT: I 83 TYR cc_start: 0.9165 (p90) cc_final: 0.8822 (p90) REVERT: J 44 GLN cc_start: 0.9302 (tp40) cc_final: 0.9034 (tp40) REVERT: K 42 ASP cc_start: 0.8603 (m-30) cc_final: 0.7985 (t70) REVERT: K 54 ASN cc_start: 0.8534 (t0) cc_final: 0.8279 (t0) REVERT: K 82 SER cc_start: 0.9585 (m) cc_final: 0.9294 (p) REVERT: K 90 ASP cc_start: 0.8929 (m-30) cc_final: 0.8351 (p0) REVERT: L 25 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8773 (mmmm) REVERT: L 37 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8698 (mtmm) REVERT: M 452 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.6176 (p90) REVERT: N 151 MET cc_start: 0.6600 (tpp) cc_final: 0.6325 (tpp) REVERT: N 277 TYR cc_start: 0.8847 (p90) cc_final: 0.8518 (p90) REVERT: N 300 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7918 (p90) REVERT: N 345 LYS cc_start: 0.9072 (mttp) cc_final: 0.8574 (mtpt) REVERT: N 412 TYR cc_start: 0.8636 (p90) cc_final: 0.8348 (p90) REVERT: N 423 ASP cc_start: 0.8941 (p0) cc_final: 0.8207 (p0) REVERT: N 428 GLU cc_start: 0.8695 (pt0) cc_final: 0.8378 (pm20) REVERT: N 499 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8778 (mt-10) REVERT: N 544 ASP cc_start: 0.8623 (t0) cc_final: 0.8371 (t0) REVERT: O 157 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7069 (ptm) REVERT: O 351 ILE cc_start: 0.9099 (pt) cc_final: 0.8642 (mt) REVERT: O 458 ILE cc_start: 0.8108 (mt) cc_final: 0.7900 (mm) REVERT: P 523 THR cc_start: 0.8708 (m) cc_final: 0.8386 (p) REVERT: P 629 PHE cc_start: 0.8618 (m-80) cc_final: 0.8225 (m-80) REVERT: Q 36 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7910 (p0) REVERT: R 179 ASN cc_start: 0.7854 (t0) cc_final: 0.7381 (t0) REVERT: T 172 MET cc_start: 0.8682 (mmm) cc_final: 0.8463 (mmm) REVERT: U 23 LEU cc_start: 0.6947 (pp) cc_final: 0.6693 (mt) REVERT: U 58 GLU cc_start: 0.8437 (tp30) cc_final: 0.7962 (tp30) REVERT: U 79 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8552 (t70) REVERT: V 49 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7816 (tm-30) REVERT: V 50 VAL cc_start: 0.9284 (t) cc_final: 0.9020 (t) REVERT: V 51 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8443 (tp30) REVERT: V 54 ASN cc_start: 0.9226 (m-40) cc_final: 0.8606 (m-40) REVERT: V 58 GLU cc_start: 0.8631 (mp0) cc_final: 0.8414 (mp0) REVERT: V 90 ASP cc_start: 0.8491 (m-30) cc_final: 0.8102 (m-30) REVERT: W 42 ASP cc_start: 0.8468 (m-30) cc_final: 0.8101 (t70) REVERT: W 51 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8636 (tp30) REVERT: W 82 SER cc_start: 0.9577 (m) cc_final: 0.9244 (p) REVERT: W 86 GLN cc_start: 0.8708 (tp40) cc_final: 0.8354 (tp40) REVERT: W 90 ASP cc_start: 0.8888 (m-30) cc_final: 0.8417 (p0) REVERT: Y 372 ASN cc_start: 0.7994 (t0) cc_final: 0.7771 (t0) REVERT: Y 452 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6726 (p90) REVERT: Y 487 PHE cc_start: 0.8833 (m-80) cc_final: 0.8387 (m-80) REVERT: Z 277 TYR cc_start: 0.8868 (p90) cc_final: 0.8605 (p90) REVERT: Z 300 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7944 (p90) REVERT: Z 351 ILE cc_start: 0.8892 (pt) cc_final: 0.8513 (mt) REVERT: Z 439 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7803 (t) REVERT: Z 499 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8498 (mt-10) REVERT: 0 182 SER cc_start: 0.9391 (m) cc_final: 0.9126 (t) REVERT: 0 247 THR cc_start: 0.9401 (p) cc_final: 0.9105 (t) REVERT: 0 351 ILE cc_start: 0.9003 (pt) cc_final: 0.8584 (mt) REVERT: 1 280 MET cc_start: 0.8371 (mmt) cc_final: 0.8150 (mmt) REVERT: 1 447 THR cc_start: 0.8607 (p) cc_final: 0.8298 (t) REVERT: 1 523 THR cc_start: 0.8397 (m) cc_final: 0.8116 (p) REVERT: 2 219 MET cc_start: 0.8499 (tpp) cc_final: 0.8006 (ttp) REVERT: 3 96 HIS cc_start: 0.8000 (m170) cc_final: 0.7744 (m-70) REVERT: 3 124 GLN cc_start: 0.7355 (tm-30) cc_final: 0.7142 (tm-30) REVERT: 4 90 HIS cc_start: 0.7625 (p-80) cc_final: 0.7178 (p-80) REVERT: 5 172 MET cc_start: 0.8272 (mmm) cc_final: 0.7889 (mmm) REVERT: 6 32 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7961 (ttp80) REVERT: 6 58 GLU cc_start: 0.7735 (mp0) cc_final: 0.7348 (mp0) REVERT: 7 89 TYR cc_start: 0.8474 (t80) cc_final: 0.8014 (t80) REVERT: 8 40 LYS cc_start: 0.8788 (tppp) cc_final: 0.8325 (tppt) REVERT: 8 42 ASP cc_start: 0.8463 (m-30) cc_final: 0.7976 (t70) REVERT: 8 82 SER cc_start: 0.9441 (m) cc_final: 0.9076 (p) REVERT: 8 86 GLN cc_start: 0.8314 (tp40) cc_final: 0.8063 (tp40) REVERT: 9 58 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8925 (mm-30) outliers start: 187 outliers final: 151 residues processed: 1151 average time/residue: 1.8649 time to fit residues: 3577.9737 Evaluate side-chains 1105 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 945 time to evaluate : 8.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 641 GLU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain M residue 645 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 291 MET Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 488 ILE Chi-restraints excluded: chain N residue 495 ASP Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 347 SER Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 456 ASP Chi-restraints excluded: chain O residue 489 THR Chi-restraints excluded: chain O residue 553 VAL Chi-restraints excluded: chain O residue 591 THR Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 183 GLU Chi-restraints excluded: chain P residue 218 VAL Chi-restraints excluded: chain P residue 275 THR Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 380 GLU Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain P residue 544 ASP Chi-restraints excluded: chain P residue 582 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain Q residue 172 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 168 ASP Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 33 GLU Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain V residue 87 ASN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 474 GLN Chi-restraints excluded: chain Y residue 482 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 641 GLU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 439 THR Chi-restraints excluded: chain Z residue 514 ASP Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 345 LYS Chi-restraints excluded: chain 0 residue 489 THR Chi-restraints excluded: chain 0 residue 513 GLN Chi-restraints excluded: chain 0 residue 591 THR Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 216 ILE Chi-restraints excluded: chain 1 residue 275 THR Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 351 ILE Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 544 ASP Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 3 residue 116 ASN Chi-restraints excluded: chain 4 residue 76 ASN Chi-restraints excluded: chain 4 residue 116 ASN Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 4 residue 180 ARG Chi-restraints excluded: chain 5 residue 42 ASP Chi-restraints excluded: chain 5 residue 113 ASP Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 82 SER Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 33 GLU Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 0.8980 chunk 533 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 699 optimal weight: 8.9990 chunk 387 optimal weight: 1.9990 chunk 801 optimal weight: 7.9990 chunk 649 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 479 optimal weight: 9.9990 chunk 843 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN ** M 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 ASN ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 GLN V 43 HIS ** V 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN ** Y 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 474 GLN Z 192 GLN Z 461 ASN ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 54 ASN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 77949 Z= 0.211 Angle : 0.566 8.214 106047 Z= 0.292 Chirality : 0.044 0.171 11823 Planarity : 0.004 0.057 13761 Dihedral : 5.949 44.091 10666 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.61 % Favored : 89.30 % Rotamer: Outliers : 2.05 % Allowed : 10.58 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.08), residues: 9759 helix: -1.17 (0.14), residues: 1239 sheet: -2.58 (0.09), residues: 2547 loop : -2.37 (0.08), residues: 5973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 477 HIS 0.008 0.001 HIS V 43 PHE 0.027 0.001 PHE D 642 TYR 0.019 0.001 TYR L 89 ARG 0.008 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1182 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1009 time to evaluate : 8.992 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 372 ASN cc_start: 0.8632 (t0) cc_final: 0.8403 (t0) REVERT: A 380 GLU cc_start: 0.8517 (tt0) cc_final: 0.8124 (tt0) REVERT: A 467 MET cc_start: 0.8970 (mtt) cc_final: 0.8390 (mtt) REVERT: A 520 GLU cc_start: 0.8214 (pm20) cc_final: 0.7890 (pm20) REVERT: B 151 MET cc_start: 0.8237 (mmm) cc_final: 0.8003 (tpp) REVERT: B 332 MET cc_start: 0.6035 (mmt) cc_final: 0.5646 (mtt) REVERT: B 345 LYS cc_start: 0.9234 (mmtp) cc_final: 0.8864 (mtpt) REVERT: B 351 ILE cc_start: 0.8867 (pt) cc_final: 0.8636 (mt) REVERT: B 428 GLU cc_start: 0.8592 (pt0) cc_final: 0.8134 (pm20) REVERT: C 157 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7453 (ptt) REVERT: C 247 THR cc_start: 0.9424 (p) cc_final: 0.9120 (t) REVERT: C 297 ILE cc_start: 0.8814 (mt) cc_final: 0.8592 (mm) REVERT: C 351 ILE cc_start: 0.9053 (pt) cc_final: 0.8683 (mt) REVERT: C 458 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7707 (mm) REVERT: D 523 THR cc_start: 0.8590 (m) cc_final: 0.8312 (p) REVERT: E 219 MET cc_start: 0.8462 (tpp) cc_final: 0.7958 (pmm) REVERT: F 133 LYS cc_start: 0.9044 (tttt) cc_final: 0.8486 (tmtt) REVERT: F 228 MET cc_start: 0.7743 (tpp) cc_final: 0.7458 (tpp) REVERT: H 56 ASN cc_start: 0.8645 (t0) cc_final: 0.8436 (t0) REVERT: I 58 GLU cc_start: 0.8266 (tp30) cc_final: 0.7286 (tp30) REVERT: I 62 GLN cc_start: 0.8726 (tp40) cc_final: 0.8472 (tp40) REVERT: I 83 TYR cc_start: 0.9169 (p90) cc_final: 0.8810 (p90) REVERT: I 98 LEU cc_start: 0.7423 (mm) cc_final: 0.7214 (mm) REVERT: K 42 ASP cc_start: 0.8598 (m-30) cc_final: 0.8026 (t70) REVERT: K 54 ASN cc_start: 0.8510 (t0) cc_final: 0.8234 (t0) REVERT: K 82 SER cc_start: 0.9582 (m) cc_final: 0.9292 (p) REVERT: K 90 ASP cc_start: 0.8759 (m-30) cc_final: 0.8349 (p0) REVERT: L 25 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8800 (mmmm) REVERT: M 573 LYS cc_start: 0.8775 (mttm) cc_final: 0.8555 (mtmt) REVERT: N 151 MET cc_start: 0.6624 (tpp) cc_final: 0.6332 (tpp) REVERT: N 277 TYR cc_start: 0.8879 (p90) cc_final: 0.8574 (p90) REVERT: N 300 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7972 (p90) REVERT: N 345 LYS cc_start: 0.9106 (mttp) cc_final: 0.8610 (mtpt) REVERT: N 412 TYR cc_start: 0.8672 (p90) cc_final: 0.8438 (p90) REVERT: N 423 ASP cc_start: 0.9005 (p0) cc_final: 0.8199 (p0) REVERT: N 424 THR cc_start: 0.9416 (m) cc_final: 0.9196 (m) REVERT: N 428 GLU cc_start: 0.8773 (pt0) cc_final: 0.8457 (pm20) REVERT: N 544 ASP cc_start: 0.8629 (t0) cc_final: 0.8351 (t0) REVERT: N 609 VAL cc_start: 0.8388 (t) cc_final: 0.8079 (m) REVERT: O 157 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6754 (ptm) REVERT: O 247 THR cc_start: 0.9265 (p) cc_final: 0.8934 (t) REVERT: O 351 ILE cc_start: 0.9025 (pt) cc_final: 0.8620 (mt) REVERT: P 523 THR cc_start: 0.8736 (m) cc_final: 0.8449 (p) REVERT: P 629 PHE cc_start: 0.8659 (m-80) cc_final: 0.8217 (m-80) REVERT: Q 36 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7894 (p0) REVERT: R 179 ASN cc_start: 0.7859 (t0) cc_final: 0.7418 (t0) REVERT: U 23 LEU cc_start: 0.6948 (pp) cc_final: 0.6673 (mt) REVERT: U 58 GLU cc_start: 0.8477 (tp30) cc_final: 0.8002 (tp30) REVERT: U 79 ASP cc_start: 0.8778 (t0) cc_final: 0.8565 (t70) REVERT: U 83 TYR cc_start: 0.9174 (p90) cc_final: 0.8879 (p90) REVERT: V 50 VAL cc_start: 0.9328 (t) cc_final: 0.9107 (t) REVERT: V 51 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8504 (tp30) REVERT: V 54 ASN cc_start: 0.9298 (m-40) cc_final: 0.8611 (m-40) REVERT: V 58 GLU cc_start: 0.8628 (mp0) cc_final: 0.8409 (mp0) REVERT: V 65 ILE cc_start: 0.8440 (pt) cc_final: 0.8237 (mt) REVERT: W 42 ASP cc_start: 0.8415 (m-30) cc_final: 0.8145 (t70) REVERT: W 82 SER cc_start: 0.9593 (m) cc_final: 0.9253 (p) REVERT: W 86 GLN cc_start: 0.8691 (tp40) cc_final: 0.8352 (tp40) REVERT: W 90 ASP cc_start: 0.8755 (m-30) cc_final: 0.8368 (p0) REVERT: Y 372 ASN cc_start: 0.8065 (t0) cc_final: 0.7849 (t0) REVERT: Y 452 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6648 (p90) REVERT: Y 467 MET cc_start: 0.8615 (mtt) cc_final: 0.8294 (mtm) REVERT: Y 487 PHE cc_start: 0.8856 (m-80) cc_final: 0.8396 (m-80) REVERT: Z 277 TYR cc_start: 0.8886 (p90) cc_final: 0.8623 (p90) REVERT: Z 351 ILE cc_start: 0.8864 (pt) cc_final: 0.8503 (mt) REVERT: Z 412 TYR cc_start: 0.8782 (p90) cc_final: 0.8513 (p90) REVERT: Z 439 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7759 (t) REVERT: Z 499 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8513 (mt-10) REVERT: 0 182 SER cc_start: 0.9388 (m) cc_final: 0.9123 (t) REVERT: 0 247 THR cc_start: 0.9400 (p) cc_final: 0.9132 (t) REVERT: 0 351 ILE cc_start: 0.8988 (pt) cc_final: 0.8595 (mt) REVERT: 0 458 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7782 (mm) REVERT: 1 182 SER cc_start: 0.9263 (m) cc_final: 0.8805 (t) REVERT: 1 447 THR cc_start: 0.8587 (p) cc_final: 0.8340 (t) REVERT: 1 523 THR cc_start: 0.8513 (m) cc_final: 0.8250 (p) REVERT: 2 219 MET cc_start: 0.8521 (tpp) cc_final: 0.8032 (ttp) REVERT: 3 96 HIS cc_start: 0.7956 (m170) cc_final: 0.7701 (m-70) REVERT: 3 124 GLN cc_start: 0.7459 (tm-30) cc_final: 0.7247 (tm-30) REVERT: 4 90 HIS cc_start: 0.7566 (p-80) cc_final: 0.7171 (p-80) REVERT: 5 172 MET cc_start: 0.8274 (mmm) cc_final: 0.7874 (mmm) REVERT: 5 219 MET cc_start: 0.8686 (ttm) cc_final: 0.8418 (ttp) REVERT: 6 32 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8050 (ttp80) REVERT: 6 58 GLU cc_start: 0.7651 (mp0) cc_final: 0.7265 (mp0) REVERT: 7 89 TYR cc_start: 0.8457 (t80) cc_final: 0.7992 (t80) REVERT: 8 40 LYS cc_start: 0.8778 (tppp) cc_final: 0.8302 (tppt) REVERT: 8 42 ASP cc_start: 0.8420 (m-30) cc_final: 0.8043 (t70) REVERT: 8 82 SER cc_start: 0.9491 (m) cc_final: 0.9156 (p) REVERT: 9 37 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8932 (mmmt) REVERT: 9 51 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7861 (pt0) REVERT: 9 58 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8916 (mm-30) outliers start: 173 outliers final: 144 residues processed: 1138 average time/residue: 1.8640 time to fit residues: 3508.3853 Evaluate side-chains 1106 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 954 time to evaluate : 8.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 340 SER Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 488 ILE Chi-restraints excluded: chain N residue 495 ASP Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 337 SER Chi-restraints excluded: chain O residue 347 SER Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 396 ILE Chi-restraints excluded: chain O residue 456 ASP Chi-restraints excluded: chain O residue 489 THR Chi-restraints excluded: chain O residue 553 VAL Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 183 GLU Chi-restraints excluded: chain P residue 275 THR Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 380 GLU Chi-restraints excluded: chain P residue 507 THR Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain P residue 544 ASP Chi-restraints excluded: chain P residue 582 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain Q residue 172 MET Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 33 GLU Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 474 GLN Chi-restraints excluded: chain Y residue 482 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 641 GLU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 331 SER Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 439 THR Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 345 LYS Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 458 ILE Chi-restraints excluded: chain 0 residue 489 THR Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 265 VAL Chi-restraints excluded: chain 1 residue 275 THR Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 351 ILE Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 544 ASP Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 3 residue 116 ASN Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 4 residue 180 ARG Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 82 SER Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 33 GLU Chi-restraints excluded: chain 7 residue 47 ASN Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 67 SER Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 316 optimal weight: 1.9990 chunk 846 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 551 optimal weight: 30.0000 chunk 231 optimal weight: 7.9990 chunk 940 optimal weight: 20.0000 chunk 780 optimal weight: 10.0000 chunk 435 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 493 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN ** M 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 HIS V 44 GLN ** V 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 GLN Z 192 GLN ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 513 GLN ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 124 GLN ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 86 GLN 7 30 GLN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 43 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 77949 Z= 0.245 Angle : 0.566 7.470 106047 Z= 0.293 Chirality : 0.044 0.160 11823 Planarity : 0.004 0.056 13761 Dihedral : 5.793 45.994 10657 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.42 % Favored : 88.49 % Rotamer: Outliers : 2.33 % Allowed : 10.87 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.08), residues: 9759 helix: -0.87 (0.14), residues: 1236 sheet: -2.46 (0.09), residues: 2520 loop : -2.31 (0.08), residues: 6003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 4 204 HIS 0.007 0.001 HIS V 43 PHE 0.022 0.001 PHE D 642 TYR 0.015 0.001 TYR 7 89 ARG 0.011 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1176 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 980 time to evaluate : 8.931 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 372 ASN cc_start: 0.8686 (t0) cc_final: 0.8474 (t0) REVERT: A 380 GLU cc_start: 0.8514 (tt0) cc_final: 0.8139 (tt0) REVERT: A 467 MET cc_start: 0.9125 (mtt) cc_final: 0.8603 (mtt) REVERT: A 520 GLU cc_start: 0.8327 (pm20) cc_final: 0.8073 (pm20) REVERT: B 151 MET cc_start: 0.8313 (mmm) cc_final: 0.8099 (tpp) REVERT: B 332 MET cc_start: 0.5794 (mmt) cc_final: 0.5526 (mtt) REVERT: B 345 LYS cc_start: 0.9257 (mmtp) cc_final: 0.8945 (mtpt) REVERT: B 351 ILE cc_start: 0.8860 (pt) cc_final: 0.8638 (mt) REVERT: B 428 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: B 609 VAL cc_start: 0.8554 (t) cc_final: 0.8309 (m) REVERT: C 157 MET cc_start: 0.7724 (ptm) cc_final: 0.7515 (ptt) REVERT: C 247 THR cc_start: 0.9397 (p) cc_final: 0.9138 (t) REVERT: C 297 ILE cc_start: 0.8850 (mt) cc_final: 0.8623 (mm) REVERT: C 351 ILE cc_start: 0.9041 (pt) cc_final: 0.8671 (mt) REVERT: D 523 THR cc_start: 0.8640 (m) cc_final: 0.8376 (p) REVERT: E 219 MET cc_start: 0.8487 (tpp) cc_final: 0.8006 (pmm) REVERT: F 133 LYS cc_start: 0.9050 (tttt) cc_final: 0.8486 (tmtt) REVERT: H 56 ASN cc_start: 0.8646 (t0) cc_final: 0.8428 (t0) REVERT: H 174 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8559 (tm) REVERT: I 58 GLU cc_start: 0.8286 (tp30) cc_final: 0.7326 (tp30) REVERT: I 62 GLN cc_start: 0.8784 (tp40) cc_final: 0.8522 (tp40) REVERT: I 83 TYR cc_start: 0.9214 (p90) cc_final: 0.8840 (p90) REVERT: J 58 GLU cc_start: 0.8083 (mp0) cc_final: 0.7870 (mp0) REVERT: K 42 ASP cc_start: 0.8605 (m-30) cc_final: 0.8041 (t70) REVERT: K 54 ASN cc_start: 0.8546 (t0) cc_final: 0.8253 (t0) REVERT: K 82 SER cc_start: 0.9593 (m) cc_final: 0.9293 (p) REVERT: K 90 ASP cc_start: 0.8731 (m-30) cc_final: 0.8342 (p0) REVERT: L 25 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8836 (mmmm) REVERT: M 151 MET cc_start: 0.7903 (tpt) cc_final: 0.7524 (tpt) REVERT: N 151 MET cc_start: 0.6674 (tpp) cc_final: 0.6397 (tpp) REVERT: N 277 TYR cc_start: 0.8883 (p90) cc_final: 0.8603 (p90) REVERT: N 300 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7959 (p90) REVERT: N 345 LYS cc_start: 0.9074 (mttp) cc_final: 0.8601 (mtpt) REVERT: N 428 GLU cc_start: 0.8795 (pt0) cc_final: 0.8508 (pm20) REVERT: N 544 ASP cc_start: 0.8685 (t0) cc_final: 0.8378 (t0) REVERT: N 609 VAL cc_start: 0.8386 (t) cc_final: 0.8107 (m) REVERT: O 157 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6797 (ptm) REVERT: O 247 THR cc_start: 0.9267 (p) cc_final: 0.8979 (t) REVERT: O 640 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8111 (pp) REVERT: P 523 THR cc_start: 0.8757 (m) cc_final: 0.8481 (p) REVERT: P 629 PHE cc_start: 0.8713 (m-80) cc_final: 0.8241 (m-80) REVERT: Q 36 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7842 (p0) REVERT: R 179 ASN cc_start: 0.7828 (t0) cc_final: 0.7482 (t0) REVERT: T 172 MET cc_start: 0.8710 (mmm) cc_final: 0.8286 (mmm) REVERT: U 23 LEU cc_start: 0.6933 (pp) cc_final: 0.6662 (mt) REVERT: U 58 GLU cc_start: 0.8469 (tp30) cc_final: 0.8021 (tp30) REVERT: U 79 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8555 (t70) REVERT: U 83 TYR cc_start: 0.9150 (p90) cc_final: 0.8902 (p90) REVERT: V 50 VAL cc_start: 0.9362 (t) cc_final: 0.9140 (t) REVERT: V 51 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8532 (tp30) REVERT: V 54 ASN cc_start: 0.9297 (m-40) cc_final: 0.8603 (m-40) REVERT: V 58 GLU cc_start: 0.8622 (mp0) cc_final: 0.8396 (mp0) REVERT: V 89 TYR cc_start: 0.8561 (t80) cc_final: 0.8292 (t80) REVERT: W 42 ASP cc_start: 0.8493 (m-30) cc_final: 0.8159 (t70) REVERT: W 82 SER cc_start: 0.9615 (m) cc_final: 0.9275 (p) REVERT: W 86 GLN cc_start: 0.8757 (tp40) cc_final: 0.8492 (tp40) REVERT: W 90 ASP cc_start: 0.8842 (m-30) cc_final: 0.8442 (p0) REVERT: W 92 GLN cc_start: 0.8804 (mt0) cc_final: 0.8576 (mp10) REVERT: X 37 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8702 (mtmm) REVERT: Y 372 ASN cc_start: 0.8161 (t0) cc_final: 0.7930 (t0) REVERT: Y 452 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.6702 (p90) REVERT: Y 467 MET cc_start: 0.8778 (mtt) cc_final: 0.8564 (mtp) REVERT: Y 487 PHE cc_start: 0.8863 (m-80) cc_final: 0.8346 (m-80) REVERT: Y 640 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7743 (pp) REVERT: Y 641 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: Z 277 TYR cc_start: 0.8882 (p90) cc_final: 0.8651 (p90) REVERT: Z 345 LYS cc_start: 0.9303 (mptt) cc_final: 0.8760 (mmmt) REVERT: Z 351 ILE cc_start: 0.8855 (pt) cc_final: 0.8500 (mt) REVERT: Z 439 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7544 (t) REVERT: Z 499 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8536 (mt-10) REVERT: Z 640 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8013 (pp) REVERT: 0 182 SER cc_start: 0.9355 (m) cc_final: 0.9097 (t) REVERT: 0 247 THR cc_start: 0.9421 (p) cc_final: 0.9175 (t) REVERT: 0 351 ILE cc_start: 0.8985 (pt) cc_final: 0.8617 (mt) REVERT: 1 157 MET cc_start: 0.8030 (ttp) cc_final: 0.7102 (ttp) REVERT: 1 182 SER cc_start: 0.9329 (m) cc_final: 0.8877 (t) REVERT: 1 447 THR cc_start: 0.8617 (p) cc_final: 0.8321 (t) REVERT: 1 523 THR cc_start: 0.8511 (m) cc_final: 0.8275 (p) REVERT: 2 219 MET cc_start: 0.8530 (tpp) cc_final: 0.8057 (ttp) REVERT: 3 219 MET cc_start: 0.7936 (tmm) cc_final: 0.7604 (tmm) REVERT: 4 90 HIS cc_start: 0.7559 (p-80) cc_final: 0.7181 (p-80) REVERT: 5 172 MET cc_start: 0.8291 (mmm) cc_final: 0.7882 (mmm) REVERT: 5 219 MET cc_start: 0.8669 (ttm) cc_final: 0.8397 (ttp) REVERT: 6 32 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8131 (ttp80) REVERT: 6 58 GLU cc_start: 0.7669 (mp0) cc_final: 0.7286 (mp0) REVERT: 7 89 TYR cc_start: 0.8440 (t80) cc_final: 0.7952 (t80) REVERT: 8 40 LYS cc_start: 0.8802 (tppp) cc_final: 0.8334 (tppt) REVERT: 8 42 ASP cc_start: 0.8493 (m-30) cc_final: 0.8052 (t70) REVERT: 8 82 SER cc_start: 0.9487 (m) cc_final: 0.9149 (p) REVERT: 9 37 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8924 (mmmt) REVERT: 9 58 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8883 (mm-30) outliers start: 196 outliers final: 165 residues processed: 1124 average time/residue: 1.8662 time to fit residues: 3504.2785 Evaluate side-chains 1118 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 941 time to evaluate : 8.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 170 PHE Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 340 SER Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain M residue 645 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 488 ILE Chi-restraints excluded: chain N residue 495 ASP Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain N residue 641 GLU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 337 SER Chi-restraints excluded: chain O residue 347 SER Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 456 ASP Chi-restraints excluded: chain O residue 489 THR Chi-restraints excluded: chain O residue 553 VAL Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 275 THR Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 380 GLU Chi-restraints excluded: chain P residue 544 ASP Chi-restraints excluded: chain P residue 582 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain Q residue 172 MET Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 31 TYR Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 33 GLU Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain Y residue 275 THR Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 445 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 482 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 641 GLU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Y residue 645 THR Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 331 SER Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 439 THR Chi-restraints excluded: chain Z residue 465 LYS Chi-restraints excluded: chain Z residue 495 ASP Chi-restraints excluded: chain Z residue 514 ASP Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 345 LYS Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 489 THR Chi-restraints excluded: chain 0 residue 591 THR Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 265 VAL Chi-restraints excluded: chain 1 residue 275 THR Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 351 ILE Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 507 THR Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 544 ASP Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 1 residue 622 ILE Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 3 residue 116 ASN Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 4 residue 180 ARG Chi-restraints excluded: chain 5 residue 113 ASP Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 82 SER Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 33 GLU Chi-restraints excluded: chain 7 residue 47 ASN Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 8 residue 47 ASN Chi-restraints excluded: chain 8 residue 96 ILE Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 67 SER Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 906 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 535 optimal weight: 9.9990 chunk 686 optimal weight: 2.9990 chunk 532 optimal weight: 1.9990 chunk 791 optimal weight: 10.0000 chunk 525 optimal weight: 8.9990 chunk 936 optimal weight: 0.0020 chunk 586 optimal weight: 2.9990 chunk 571 optimal weight: 8.9990 chunk 432 optimal weight: 9.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** M 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 43 HIS ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 96 HIS 4 124 GLN ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 77949 Z= 0.234 Angle : 0.558 8.120 106047 Z= 0.288 Chirality : 0.044 0.157 11823 Planarity : 0.004 0.059 13761 Dihedral : 5.675 46.416 10654 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.15 % Favored : 88.78 % Rotamer: Outliers : 2.36 % Allowed : 11.05 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.08), residues: 9759 helix: -0.60 (0.15), residues: 1236 sheet: -2.37 (0.09), residues: 2559 loop : -2.20 (0.08), residues: 5964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 179 HIS 0.007 0.001 HIS S 90 PHE 0.028 0.001 PHE D 642 TYR 0.033 0.001 TYR N 252 ARG 0.012 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1157 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 958 time to evaluate : 8.977 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 372 ASN cc_start: 0.8726 (t0) cc_final: 0.8492 (t0) REVERT: A 380 GLU cc_start: 0.8514 (tt0) cc_final: 0.8123 (tt0) REVERT: A 467 MET cc_start: 0.9166 (mtt) cc_final: 0.8625 (mtt) REVERT: B 151 MET cc_start: 0.8356 (mmm) cc_final: 0.8087 (tpp) REVERT: B 332 MET cc_start: 0.5816 (mmt) cc_final: 0.5510 (mtt) REVERT: B 345 LYS cc_start: 0.9271 (mmtp) cc_final: 0.8974 (mtpt) REVERT: B 428 GLU cc_start: 0.8636 (pt0) cc_final: 0.8237 (pm20) REVERT: B 609 VAL cc_start: 0.8562 (t) cc_final: 0.8341 (m) REVERT: C 157 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7516 (ptt) REVERT: C 247 THR cc_start: 0.9383 (p) cc_final: 0.9156 (t) REVERT: C 351 ILE cc_start: 0.9022 (pt) cc_final: 0.8681 (mt) REVERT: C 458 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7678 (mm) REVERT: D 523 THR cc_start: 0.8670 (m) cc_final: 0.8451 (p) REVERT: E 219 MET cc_start: 0.8495 (tpp) cc_final: 0.8034 (pmm) REVERT: F 124 GLN cc_start: 0.7510 (tm-30) cc_final: 0.6960 (tm-30) REVERT: F 133 LYS cc_start: 0.9044 (tttt) cc_final: 0.8481 (tmtt) REVERT: H 56 ASN cc_start: 0.8653 (t0) cc_final: 0.8447 (t0) REVERT: H 174 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8577 (tm) REVERT: I 39 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7378 (mtt) REVERT: I 58 GLU cc_start: 0.8317 (tp30) cc_final: 0.7398 (tp30) REVERT: I 62 GLN cc_start: 0.8816 (tp40) cc_final: 0.8506 (tp40) REVERT: I 83 TYR cc_start: 0.9239 (p90) cc_final: 0.8864 (p90) REVERT: K 42 ASP cc_start: 0.8614 (m-30) cc_final: 0.8054 (t70) REVERT: K 54 ASN cc_start: 0.8541 (t0) cc_final: 0.8246 (t0) REVERT: K 82 SER cc_start: 0.9570 (m) cc_final: 0.9271 (p) REVERT: K 90 ASP cc_start: 0.8703 (m-30) cc_final: 0.8354 (p0) REVERT: L 25 LYS cc_start: 0.9080 (mmtp) cc_final: 0.8826 (mmmm) REVERT: M 151 MET cc_start: 0.8042 (tpt) cc_final: 0.7682 (tpt) REVERT: M 242 ASP cc_start: 0.7584 (t70) cc_final: 0.7382 (p0) REVERT: N 277 TYR cc_start: 0.8894 (p90) cc_final: 0.8627 (p90) REVERT: N 300 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7959 (p90) REVERT: N 345 LYS cc_start: 0.9076 (mttp) cc_final: 0.8530 (mtpp) REVERT: N 428 GLU cc_start: 0.8807 (pt0) cc_final: 0.8519 (pm20) REVERT: N 544 ASP cc_start: 0.8697 (t0) cc_final: 0.8380 (t0) REVERT: O 157 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6828 (ptm) REVERT: O 247 THR cc_start: 0.9269 (p) cc_final: 0.8983 (t) REVERT: O 351 ILE cc_start: 0.8948 (pt) cc_final: 0.8591 (mt) REVERT: O 640 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8236 (pp) REVERT: P 523 THR cc_start: 0.8664 (m) cc_final: 0.8418 (p) REVERT: P 629 PHE cc_start: 0.8760 (m-80) cc_final: 0.8251 (m-80) REVERT: Q 36 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7875 (p0) REVERT: R 179 ASN cc_start: 0.7809 (t0) cc_final: 0.7463 (t0) REVERT: T 172 MET cc_start: 0.8692 (mmm) cc_final: 0.8291 (mmm) REVERT: U 23 LEU cc_start: 0.6819 (pp) cc_final: 0.6518 (mt) REVERT: U 58 GLU cc_start: 0.8500 (tp30) cc_final: 0.8046 (tp30) REVERT: U 79 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8567 (t70) REVERT: V 51 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8554 (tp30) REVERT: V 58 GLU cc_start: 0.8608 (mp0) cc_final: 0.8395 (mp0) REVERT: V 89 TYR cc_start: 0.8615 (t80) cc_final: 0.8395 (t80) REVERT: W 42 ASP cc_start: 0.8483 (m-30) cc_final: 0.8167 (t70) REVERT: W 82 SER cc_start: 0.9571 (m) cc_final: 0.9221 (p) REVERT: W 86 GLN cc_start: 0.8716 (tp40) cc_final: 0.8374 (tp40) REVERT: W 90 ASP cc_start: 0.8831 (m-30) cc_final: 0.8380 (p0) REVERT: Y 283 THR cc_start: 0.8833 (p) cc_final: 0.8569 (t) REVERT: Y 372 ASN cc_start: 0.8206 (t0) cc_final: 0.7973 (t0) REVERT: Y 452 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.6750 (p90) REVERT: Y 487 PHE cc_start: 0.8873 (m-80) cc_final: 0.8323 (m-80) REVERT: Y 602 LEU cc_start: 0.8811 (tp) cc_final: 0.8560 (tt) REVERT: Y 640 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7829 (pp) REVERT: Z 277 TYR cc_start: 0.8900 (p90) cc_final: 0.8665 (p90) REVERT: Z 345 LYS cc_start: 0.9321 (mptt) cc_final: 0.8660 (mmmt) REVERT: Z 351 ILE cc_start: 0.8865 (pt) cc_final: 0.8519 (mt) REVERT: Z 439 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7430 (t) REVERT: Z 499 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8498 (mt-10) REVERT: Z 640 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8139 (pp) REVERT: 0 247 THR cc_start: 0.9422 (p) cc_final: 0.9201 (t) REVERT: 0 351 ILE cc_start: 0.8992 (pt) cc_final: 0.8623 (mt) REVERT: 0 458 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7801 (mm) REVERT: 0 640 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8046 (pp) REVERT: 1 182 SER cc_start: 0.9372 (m) cc_final: 0.8937 (t) REVERT: 1 447 THR cc_start: 0.8576 (p) cc_final: 0.8278 (t) REVERT: 1 523 THR cc_start: 0.8542 (m) cc_final: 0.8336 (p) REVERT: 2 219 MET cc_start: 0.8495 (tpp) cc_final: 0.8086 (ttp) REVERT: 3 219 MET cc_start: 0.8011 (tmm) cc_final: 0.7649 (tmm) REVERT: 4 90 HIS cc_start: 0.7534 (p-80) cc_final: 0.7154 (p-80) REVERT: 5 172 MET cc_start: 0.8291 (mmm) cc_final: 0.7754 (mmm) REVERT: 5 219 MET cc_start: 0.8639 (ttm) cc_final: 0.8383 (ttp) REVERT: 6 32 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8157 (ttp80) REVERT: 6 58 GLU cc_start: 0.7648 (mp0) cc_final: 0.7270 (mp0) REVERT: 7 89 TYR cc_start: 0.8434 (t80) cc_final: 0.7884 (t80) REVERT: 8 40 LYS cc_start: 0.8809 (tppp) cc_final: 0.8319 (tppt) REVERT: 8 42 ASP cc_start: 0.8498 (m-30) cc_final: 0.8064 (t70) REVERT: 8 82 SER cc_start: 0.9493 (m) cc_final: 0.9188 (p) REVERT: 9 51 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7976 (pt0) REVERT: 9 58 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8909 (mm-30) REVERT: 9 97 ARG cc_start: 0.8578 (mtm110) cc_final: 0.8260 (mtm-85) outliers start: 199 outliers final: 163 residues processed: 1101 average time/residue: 1.8049 time to fit residues: 3295.7161 Evaluate side-chains 1099 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 921 time to evaluate : 8.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 39 MET Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 170 PHE Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 340 SER Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 445 ASP Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain M residue 645 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 488 ILE Chi-restraints excluded: chain N residue 495 ASP Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain N residue 641 GLU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 347 SER Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 456 ASP Chi-restraints excluded: chain O residue 489 THR Chi-restraints excluded: chain O residue 553 VAL Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 183 GLU Chi-restraints excluded: chain P residue 275 THR Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 380 GLU Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain P residue 544 ASP Chi-restraints excluded: chain P residue 582 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain Q residue 172 MET Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 31 TYR Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 33 GLU Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain Y residue 275 THR Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 482 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Y residue 645 THR Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 262 VAL Chi-restraints excluded: chain Z residue 331 SER Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 439 THR Chi-restraints excluded: chain Z residue 465 LYS Chi-restraints excluded: chain Z residue 467 MET Chi-restraints excluded: chain Z residue 495 ASP Chi-restraints excluded: chain Z residue 514 ASP Chi-restraints excluded: chain Z residue 601 LEU Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 345 LYS Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 458 ILE Chi-restraints excluded: chain 0 residue 489 THR Chi-restraints excluded: chain 0 residue 546 ASP Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 265 VAL Chi-restraints excluded: chain 1 residue 275 THR Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 351 ILE Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 544 ASP Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 1 residue 622 ILE Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 3 residue 116 ASN Chi-restraints excluded: chain 4 residue 76 ASN Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 4 residue 180 ARG Chi-restraints excluded: chain 5 residue 113 ASP Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 82 SER Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 30 GLN Chi-restraints excluded: chain 7 residue 47 ASN Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 67 SER Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 9.9990 chunk 374 optimal weight: 8.9990 chunk 559 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 184 optimal weight: 0.0030 chunk 181 optimal weight: 10.0000 chunk 595 optimal weight: 6.9990 chunk 638 optimal weight: 9.9990 chunk 463 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 736 optimal weight: 9.9990 overall best weight: 7.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN I 62 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 GLN M 599 HIS ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 616 ASN R 190 ASN ** T 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 116 ASN ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 86 GLN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 77949 Z= 0.445 Angle : 0.649 8.271 106047 Z= 0.339 Chirality : 0.046 0.184 11823 Planarity : 0.005 0.077 13761 Dihedral : 5.937 49.551 10651 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.35 % Favored : 85.57 % Rotamer: Outliers : 2.65 % Allowed : 11.37 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.08), residues: 9759 helix: -0.77 (0.14), residues: 1260 sheet: -2.41 (0.10), residues: 2589 loop : -2.35 (0.08), residues: 5910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 1 179 HIS 0.009 0.002 HIS 1 590 PHE 0.028 0.002 PHE D 642 TYR 0.024 0.002 TYR N 252 ARG 0.013 0.001 ARG H 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1117 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 894 time to evaluate : 9.017 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 467 MET cc_start: 0.9274 (mtt) cc_final: 0.8750 (mtt) REVERT: B 332 MET cc_start: 0.5925 (mmt) cc_final: 0.5451 (mtt) REVERT: B 345 LYS cc_start: 0.9265 (mmtp) cc_final: 0.8990 (mtpt) REVERT: B 360 THR cc_start: 0.8625 (p) cc_final: 0.7785 (p) REVERT: B 428 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: C 458 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7787 (mm) REVERT: E 219 MET cc_start: 0.8477 (tpp) cc_final: 0.7994 (pmm) REVERT: F 124 GLN cc_start: 0.7601 (tm-30) cc_final: 0.6980 (tm-30) REVERT: F 133 LYS cc_start: 0.9090 (tttt) cc_final: 0.8588 (tmtt) REVERT: H 174 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8628 (tm) REVERT: I 58 GLU cc_start: 0.8443 (tp30) cc_final: 0.7997 (tp30) REVERT: K 42 ASP cc_start: 0.8639 (m-30) cc_final: 0.8111 (t70) REVERT: K 54 ASN cc_start: 0.8637 (t0) cc_final: 0.8367 (t0) REVERT: K 82 SER cc_start: 0.9602 (m) cc_final: 0.9315 (p) REVERT: K 90 ASP cc_start: 0.8755 (m-30) cc_final: 0.8312 (p0) REVERT: L 25 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8869 (mmmm) REVERT: M 151 MET cc_start: 0.8446 (tpt) cc_final: 0.8073 (tpt) REVERT: M 242 ASP cc_start: 0.7771 (t70) cc_final: 0.7490 (p0) REVERT: M 467 MET cc_start: 0.9076 (mtt) cc_final: 0.8697 (mtt) REVERT: N 277 TYR cc_start: 0.9038 (p90) cc_final: 0.8738 (p90) REVERT: N 300 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8126 (p90) REVERT: N 345 LYS cc_start: 0.9153 (mttp) cc_final: 0.8702 (mtpt) REVERT: N 428 GLU cc_start: 0.8815 (pt0) cc_final: 0.8535 (pm20) REVERT: N 465 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8298 (ptpt) REVERT: N 544 ASP cc_start: 0.8788 (t0) cc_final: 0.8454 (t0) REVERT: N 644 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8491 (pp) REVERT: O 157 MET cc_start: 0.7241 (ptm) cc_final: 0.6933 (ptm) REVERT: O 247 THR cc_start: 0.9359 (p) cc_final: 0.9156 (t) REVERT: O 640 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8252 (pp) REVERT: P 428 GLU cc_start: 0.8922 (pm20) cc_final: 0.8598 (pm20) REVERT: T 172 MET cc_start: 0.8694 (mmm) cc_final: 0.8273 (mmm) REVERT: U 23 LEU cc_start: 0.6727 (pp) cc_final: 0.6388 (mt) REVERT: U 58 GLU cc_start: 0.8452 (tp30) cc_final: 0.8018 (tp30) REVERT: U 79 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8688 (t70) REVERT: U 83 TYR cc_start: 0.9344 (p90) cc_final: 0.8866 (p90) REVERT: V 58 GLU cc_start: 0.8594 (mp0) cc_final: 0.8356 (mp0) REVERT: W 42 ASP cc_start: 0.8536 (m-30) cc_final: 0.8218 (t70) REVERT: W 51 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8857 (tp30) REVERT: W 82 SER cc_start: 0.9601 (m) cc_final: 0.9266 (p) REVERT: W 86 GLN cc_start: 0.8742 (tp40) cc_final: 0.8481 (tp40) REVERT: W 90 ASP cc_start: 0.8914 (m-30) cc_final: 0.8373 (p0) REVERT: Y 283 THR cc_start: 0.8868 (p) cc_final: 0.8618 (t) REVERT: Y 372 ASN cc_start: 0.8340 (t0) cc_final: 0.8080 (t0) REVERT: Z 345 LYS cc_start: 0.9353 (mptt) cc_final: 0.8804 (mmmt) REVERT: Z 351 ILE cc_start: 0.8841 (pt) cc_final: 0.8520 (mt) REVERT: Z 439 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7644 (t) REVERT: 0 157 MET cc_start: 0.8168 (ptm) cc_final: 0.7955 (ptm) REVERT: 0 247 THR cc_start: 0.9491 (p) cc_final: 0.9282 (t) REVERT: 0 372 ASN cc_start: 0.8136 (t0) cc_final: 0.7689 (t0) REVERT: 0 458 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7898 (mm) REVERT: 0 640 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8095 (pp) REVERT: 1 182 SER cc_start: 0.9497 (m) cc_final: 0.9111 (t) REVERT: 1 447 THR cc_start: 0.8644 (p) cc_final: 0.8406 (t) REVERT: 1 523 THR cc_start: 0.8695 (m) cc_final: 0.8490 (p) REVERT: 2 124 GLN cc_start: 0.8871 (pt0) cc_final: 0.8567 (pt0) REVERT: 2 219 MET cc_start: 0.8520 (tpp) cc_final: 0.8062 (ttp) REVERT: 3 124 GLN cc_start: 0.7431 (tm-30) cc_final: 0.7168 (tm-30) REVERT: 3 199 ASP cc_start: 0.7890 (m-30) cc_final: 0.7634 (m-30) REVERT: 3 219 MET cc_start: 0.8078 (tmm) cc_final: 0.7659 (tmm) REVERT: 4 90 HIS cc_start: 0.7690 (p-80) cc_final: 0.7247 (p-80) REVERT: 5 172 MET cc_start: 0.8348 (mmm) cc_final: 0.7806 (mmm) REVERT: 5 219 MET cc_start: 0.8605 (ttm) cc_final: 0.8372 (ttp) REVERT: 6 32 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8154 (ttp80) REVERT: 6 58 GLU cc_start: 0.7679 (mp0) cc_final: 0.7271 (mp0) REVERT: 7 89 TYR cc_start: 0.8598 (t80) cc_final: 0.7944 (t80) REVERT: 8 40 LYS cc_start: 0.8800 (tppp) cc_final: 0.8303 (tppt) REVERT: 8 42 ASP cc_start: 0.8550 (m-30) cc_final: 0.8060 (t70) REVERT: 8 82 SER cc_start: 0.9498 (m) cc_final: 0.9199 (p) REVERT: 9 58 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8879 (mm-30) outliers start: 223 outliers final: 189 residues processed: 1060 average time/residue: 1.8213 time to fit residues: 3225.1219 Evaluate side-chains 1061 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 861 time to evaluate : 8.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 170 PHE Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 275 THR Chi-restraints excluded: chain M residue 295 ASP Chi-restraints excluded: chain M residue 340 SER Chi-restraints excluded: chain M residue 351 ILE Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 445 ASP Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain M residue 645 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 351 ILE Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 488 ILE Chi-restraints excluded: chain N residue 495 ASP Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain N residue 641 GLU Chi-restraints excluded: chain N residue 644 LEU Chi-restraints excluded: chain O residue 337 SER Chi-restraints excluded: chain O residue 347 SER Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 438 ILE Chi-restraints excluded: chain O residue 456 ASP Chi-restraints excluded: chain O residue 489 THR Chi-restraints excluded: chain O residue 553 VAL Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 183 GLU Chi-restraints excluded: chain P residue 275 THR Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 380 GLU Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain P residue 582 ASP Chi-restraints excluded: chain P residue 622 ILE Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 31 TYR Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain S residue 196 LEU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 33 GLU Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 143 VAL Chi-restraints excluded: chain Y residue 170 PHE Chi-restraints excluded: chain Y residue 275 THR Chi-restraints excluded: chain Y residue 340 SER Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 445 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 482 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Y residue 645 THR Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 284 ASP Chi-restraints excluded: chain Z residue 331 SER Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 439 THR Chi-restraints excluded: chain Z residue 465 LYS Chi-restraints excluded: chain Z residue 467 MET Chi-restraints excluded: chain Z residue 495 ASP Chi-restraints excluded: chain Z residue 514 ASP Chi-restraints excluded: chain Z residue 601 LEU Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 345 LYS Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 435 ASP Chi-restraints excluded: chain 0 residue 458 ILE Chi-restraints excluded: chain 0 residue 464 PHE Chi-restraints excluded: chain 0 residue 489 THR Chi-restraints excluded: chain 0 residue 591 THR Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 265 VAL Chi-restraints excluded: chain 1 residue 275 THR Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 351 ILE Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 544 ASP Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 1 residue 622 ILE Chi-restraints excluded: chain 2 residue 34 GLU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 3 residue 116 ASN Chi-restraints excluded: chain 4 residue 31 TYR Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 116 ASN Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 4 residue 180 ARG Chi-restraints excluded: chain 5 residue 42 ASP Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 82 SER Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 30 GLN Chi-restraints excluded: chain 7 residue 47 ASN Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 67 SER Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 0.9990 chunk 897 optimal weight: 20.0000 chunk 818 optimal weight: 0.1980 chunk 873 optimal weight: 5.9990 chunk 525 optimal weight: 1.9990 chunk 380 optimal weight: 8.9990 chunk 685 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 788 optimal weight: 9.9990 chunk 825 optimal weight: 0.8980 chunk 869 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 190 ASN V 48 ASN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 77949 Z= 0.168 Angle : 0.557 8.497 106047 Z= 0.287 Chirality : 0.044 0.223 11823 Planarity : 0.004 0.072 13761 Dihedral : 5.667 49.871 10651 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.11 % Favored : 89.82 % Rotamer: Outliers : 1.92 % Allowed : 12.49 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.08), residues: 9759 helix: -0.41 (0.15), residues: 1251 sheet: -2.23 (0.10), residues: 2559 loop : -2.14 (0.08), residues: 5949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 204 HIS 0.008 0.001 HIS S 90 PHE 0.026 0.001 PHE A 642 TYR 0.026 0.001 TYR W 83 ARG 0.012 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1119 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 957 time to evaluate : 8.975 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 280 MET cc_start: 0.9016 (mmt) cc_final: 0.8306 (mmt) REVERT: A 467 MET cc_start: 0.9303 (mtt) cc_final: 0.8792 (mtt) REVERT: A 649 MET cc_start: 0.8831 (tpp) cc_final: 0.8588 (tpp) REVERT: B 332 MET cc_start: 0.5894 (mmt) cc_final: 0.5405 (mtt) REVERT: B 345 LYS cc_start: 0.9266 (mmtp) cc_final: 0.8970 (mtpt) REVERT: B 428 GLU cc_start: 0.8697 (pt0) cc_final: 0.8352 (pm20) REVERT: C 458 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7654 (mm) REVERT: E 219 MET cc_start: 0.8437 (tpp) cc_final: 0.7977 (pmm) REVERT: F 124 GLN cc_start: 0.7649 (tm-30) cc_final: 0.6994 (tm-30) REVERT: F 228 MET cc_start: 0.8024 (tpp) cc_final: 0.7720 (tpp) REVERT: H 174 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8593 (tm) REVERT: I 58 GLU cc_start: 0.8593 (tp30) cc_final: 0.8208 (tp30) REVERT: K 42 ASP cc_start: 0.8567 (m-30) cc_final: 0.7878 (t70) REVERT: K 54 ASN cc_start: 0.8658 (t0) cc_final: 0.8378 (t0) REVERT: K 82 SER cc_start: 0.9581 (m) cc_final: 0.9270 (p) REVERT: K 90 ASP cc_start: 0.8745 (m-30) cc_final: 0.8362 (p0) REVERT: L 25 LYS cc_start: 0.9096 (mmtp) cc_final: 0.8838 (mmmm) REVERT: M 151 MET cc_start: 0.8244 (tpt) cc_final: 0.7918 (tpt) REVERT: M 467 MET cc_start: 0.9087 (mtt) cc_final: 0.8751 (mtt) REVERT: N 277 TYR cc_start: 0.9015 (p90) cc_final: 0.8774 (p90) REVERT: N 300 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7930 (p90) REVERT: N 345 LYS cc_start: 0.9073 (mttp) cc_final: 0.8554 (mtpp) REVERT: N 428 GLU cc_start: 0.8807 (pt0) cc_final: 0.8516 (pm20) REVERT: N 544 ASP cc_start: 0.8727 (t0) cc_final: 0.8391 (t0) REVERT: N 597 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8917 (pp) REVERT: O 157 MET cc_start: 0.7147 (ptm) cc_final: 0.6850 (ptm) REVERT: O 640 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8267 (pp) REVERT: P 598 ASN cc_start: 0.9065 (m-40) cc_final: 0.8864 (m-40) REVERT: R 179 ASN cc_start: 0.7779 (t0) cc_final: 0.7040 (m-40) REVERT: R 180 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7506 (mpp80) REVERT: S 90 HIS cc_start: 0.7677 (p-80) cc_final: 0.7170 (p-80) REVERT: T 172 MET cc_start: 0.8647 (mmm) cc_final: 0.8269 (mmm) REVERT: U 23 LEU cc_start: 0.6736 (pp) cc_final: 0.6383 (mt) REVERT: U 58 GLU cc_start: 0.8521 (tp30) cc_final: 0.8079 (tp30) REVERT: U 79 ASP cc_start: 0.8844 (t0) cc_final: 0.8642 (t70) REVERT: U 83 TYR cc_start: 0.9330 (p90) cc_final: 0.8886 (p90) REVERT: V 58 GLU cc_start: 0.8487 (mp0) cc_final: 0.8226 (mp0) REVERT: W 42 ASP cc_start: 0.8458 (m-30) cc_final: 0.8153 (t70) REVERT: W 51 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8835 (tp30) REVERT: W 82 SER cc_start: 0.9556 (m) cc_final: 0.9218 (p) REVERT: W 86 GLN cc_start: 0.8696 (tp40) cc_final: 0.8439 (tp40) REVERT: W 90 ASP cc_start: 0.8809 (m-30) cc_final: 0.8363 (p0) REVERT: Y 283 THR cc_start: 0.8844 (p) cc_final: 0.8603 (t) REVERT: Y 372 ASN cc_start: 0.8257 (t0) cc_final: 0.8029 (t0) REVERT: Y 640 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7913 (pp) REVERT: Z 277 TYR cc_start: 0.8910 (p90) cc_final: 0.8703 (p90) REVERT: Z 280 MET cc_start: 0.9016 (mmt) cc_final: 0.8261 (mmt) REVERT: Z 345 LYS cc_start: 0.9330 (mptt) cc_final: 0.8806 (mmmt) REVERT: Z 351 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8502 (mt) REVERT: Z 439 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7365 (t) REVERT: 0 351 ILE cc_start: 0.8894 (pt) cc_final: 0.8602 (mt) REVERT: 0 458 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7798 (mm) REVERT: 0 640 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8071 (pp) REVERT: 1 182 SER cc_start: 0.9408 (m) cc_final: 0.8976 (t) REVERT: 1 447 THR cc_start: 0.8556 (p) cc_final: 0.8298 (t) REVERT: 2 219 MET cc_start: 0.8500 (tpp) cc_final: 0.8049 (ttp) REVERT: 3 124 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7132 (tm-30) REVERT: 3 219 MET cc_start: 0.8065 (tmm) cc_final: 0.7669 (tmm) REVERT: 4 90 HIS cc_start: 0.7588 (p-80) cc_final: 0.7233 (p-80) REVERT: 5 172 MET cc_start: 0.8335 (mmm) cc_final: 0.7769 (mmm) REVERT: 6 58 GLU cc_start: 0.7663 (mp0) cc_final: 0.7307 (mp0) REVERT: 7 89 TYR cc_start: 0.8459 (t80) cc_final: 0.7780 (t80) REVERT: 8 40 LYS cc_start: 0.8789 (tppp) cc_final: 0.8290 (tppt) REVERT: 8 42 ASP cc_start: 0.8466 (m-30) cc_final: 0.8042 (t70) REVERT: 8 82 SER cc_start: 0.9463 (m) cc_final: 0.9147 (p) REVERT: 9 58 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8871 (mm-30) REVERT: 9 97 ARG cc_start: 0.8564 (mtm110) cc_final: 0.8166 (mtm-85) outliers start: 162 outliers final: 136 residues processed: 1071 average time/residue: 1.8269 time to fit residues: 3259.3676 Evaluate side-chains 1049 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 902 time to evaluate : 8.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 170 PHE Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 445 ASP Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 488 ILE Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain N residue 641 GLU Chi-restraints excluded: chain O residue 337 SER Chi-restraints excluded: chain O residue 347 SER Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 438 ILE Chi-restraints excluded: chain O residue 456 ASP Chi-restraints excluded: chain O residue 489 THR Chi-restraints excluded: chain O residue 553 VAL Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 183 GLU Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain P residue 582 ASP Chi-restraints excluded: chain P residue 622 ILE Chi-restraints excluded: chain Q residue 31 TYR Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 180 ARG Chi-restraints excluded: chain S residue 31 TYR Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain Y residue 275 THR Chi-restraints excluded: chain Y residue 340 SER Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 482 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 351 ILE Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 439 THR Chi-restraints excluded: chain Z residue 465 LYS Chi-restraints excluded: chain Z residue 495 ASP Chi-restraints excluded: chain Z residue 601 LEU Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 242 ASP Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 458 ILE Chi-restraints excluded: chain 0 residue 489 THR Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 265 VAL Chi-restraints excluded: chain 1 residue 275 THR Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 351 ILE Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 544 ASP Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 1 residue 622 ILE Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 3 residue 116 ASN Chi-restraints excluded: chain 4 residue 31 TYR Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 4 residue 180 ARG Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 82 SER Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 30 GLN Chi-restraints excluded: chain 7 residue 47 ASN Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 67 SER Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 573 optimal weight: 6.9990 chunk 923 optimal weight: 10.0000 chunk 563 optimal weight: 9.9990 chunk 437 optimal weight: 6.9990 chunk 641 optimal weight: 9.9990 chunk 968 optimal weight: 10.0000 chunk 891 optimal weight: 20.0000 chunk 771 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 595 optimal weight: 8.9990 chunk 472 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 86 GLN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 77949 Z= 0.343 Angle : 0.601 9.697 106047 Z= 0.312 Chirality : 0.045 0.234 11823 Planarity : 0.004 0.073 13761 Dihedral : 5.732 52.097 10649 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.29 % Favored : 86.64 % Rotamer: Outliers : 1.86 % Allowed : 12.84 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.08), residues: 9759 helix: -0.43 (0.15), residues: 1248 sheet: -2.19 (0.10), residues: 2562 loop : -2.19 (0.08), residues: 5949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 179 HIS 0.008 0.001 HIS S 90 PHE 0.031 0.002 PHE P 642 TYR 0.022 0.001 TYR W 83 ARG 0.014 0.001 ARG R 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19518 Ramachandran restraints generated. 9759 Oldfield, 0 Emsley, 9759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Residue ALA 402 is missing expected H atoms. Skipping. Residue THR 431 is missing expected H atoms. Skipping. Evaluate side-chains 1046 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 889 time to evaluate : 8.953 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 467 MET cc_start: 0.9309 (mtt) cc_final: 0.8799 (mtt) REVERT: B 332 MET cc_start: 0.5951 (mmt) cc_final: 0.5422 (mtt) REVERT: B 345 LYS cc_start: 0.9281 (mmtp) cc_final: 0.8996 (mtpt) REVERT: B 428 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: C 225 SER cc_start: 0.8784 (p) cc_final: 0.8549 (t) REVERT: C 458 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7712 (mm) REVERT: D 242 ASP cc_start: 0.8244 (t0) cc_final: 0.7923 (t70) REVERT: E 219 MET cc_start: 0.8459 (tpp) cc_final: 0.7992 (pmm) REVERT: F 228 MET cc_start: 0.7992 (tpp) cc_final: 0.7700 (tpp) REVERT: H 174 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8586 (tm) REVERT: I 58 GLU cc_start: 0.8596 (tp30) cc_final: 0.8206 (tp30) REVERT: K 42 ASP cc_start: 0.8634 (m-30) cc_final: 0.7986 (t70) REVERT: K 54 ASN cc_start: 0.8721 (t0) cc_final: 0.8469 (t0) REVERT: K 66 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8799 (tm-30) REVERT: K 82 SER cc_start: 0.9606 (m) cc_final: 0.9314 (p) REVERT: K 90 ASP cc_start: 0.8786 (m-30) cc_final: 0.8276 (p0) REVERT: L 25 LYS cc_start: 0.9097 (mmtp) cc_final: 0.8855 (mmmm) REVERT: M 151 MET cc_start: 0.8515 (tpt) cc_final: 0.8176 (tpt) REVERT: M 467 MET cc_start: 0.9084 (mtt) cc_final: 0.8717 (mtt) REVERT: N 277 TYR cc_start: 0.9020 (p90) cc_final: 0.8764 (p90) REVERT: N 300 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.8066 (p90) REVERT: N 345 LYS cc_start: 0.9140 (mttp) cc_final: 0.8726 (mtpt) REVERT: N 428 GLU cc_start: 0.8778 (pt0) cc_final: 0.8457 (pm20) REVERT: N 465 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8249 (ptpt) REVERT: N 544 ASP cc_start: 0.8774 (t0) cc_final: 0.8441 (t0) REVERT: O 157 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6883 (ptm) REVERT: O 640 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8278 (pp) REVERT: P 531 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8925 (tm) REVERT: P 598 ASN cc_start: 0.9099 (m-40) cc_final: 0.8866 (m-40) REVERT: R 179 ASN cc_start: 0.7866 (t0) cc_final: 0.7113 (m-40) REVERT: S 100 ARG cc_start: 0.8839 (ptp90) cc_final: 0.8548 (ttm110) REVERT: T 172 MET cc_start: 0.8647 (mmm) cc_final: 0.8269 (mmm) REVERT: T 180 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7911 (mmt180) REVERT: U 23 LEU cc_start: 0.6699 (pp) cc_final: 0.6320 (mt) REVERT: U 58 GLU cc_start: 0.8487 (tp30) cc_final: 0.8123 (tp30) REVERT: U 83 TYR cc_start: 0.9355 (p90) cc_final: 0.8908 (p90) REVERT: V 58 GLU cc_start: 0.8554 (mp0) cc_final: 0.8329 (mp0) REVERT: W 42 ASP cc_start: 0.8498 (m-30) cc_final: 0.8184 (t70) REVERT: W 51 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8891 (tp30) REVERT: W 82 SER cc_start: 0.9573 (m) cc_final: 0.9267 (p) REVERT: W 86 GLN cc_start: 0.8721 (tp40) cc_final: 0.8417 (tp40) REVERT: W 90 ASP cc_start: 0.8827 (m-30) cc_final: 0.8334 (p0) REVERT: Y 283 THR cc_start: 0.8873 (p) cc_final: 0.8628 (t) REVERT: Y 372 ASN cc_start: 0.8421 (t0) cc_final: 0.8201 (t0) REVERT: Y 640 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7880 (pp) REVERT: Z 280 MET cc_start: 0.9067 (mmt) cc_final: 0.8288 (mmt) REVERT: Z 345 LYS cc_start: 0.9333 (mptt) cc_final: 0.8808 (mmmt) REVERT: Z 351 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8488 (mt) REVERT: Z 439 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7567 (t) REVERT: Z 490 THR cc_start: 0.9445 (m) cc_final: 0.9239 (p) REVERT: 0 157 MET cc_start: 0.8028 (ptm) cc_final: 0.7666 (ptm) REVERT: 0 372 ASN cc_start: 0.8101 (t0) cc_final: 0.7642 (t0) REVERT: 0 458 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7882 (mm) REVERT: 0 640 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8089 (pp) REVERT: 1 242 ASP cc_start: 0.8130 (t0) cc_final: 0.7795 (t70) REVERT: 1 447 THR cc_start: 0.8529 (p) cc_final: 0.8315 (t) REVERT: 2 124 GLN cc_start: 0.8917 (pt0) cc_final: 0.8650 (pt0) REVERT: 2 219 MET cc_start: 0.8501 (tpp) cc_final: 0.8058 (ttp) REVERT: 3 219 MET cc_start: 0.8092 (tmm) cc_final: 0.7594 (tmm) REVERT: 4 90 HIS cc_start: 0.7641 (p-80) cc_final: 0.7257 (p-80) REVERT: 5 172 MET cc_start: 0.8370 (mmm) cc_final: 0.7790 (mmm) REVERT: 6 58 GLU cc_start: 0.7665 (mp0) cc_final: 0.7299 (mp0) REVERT: 7 89 TYR cc_start: 0.8513 (t80) cc_final: 0.7842 (t80) REVERT: 8 40 LYS cc_start: 0.8798 (tppp) cc_final: 0.8300 (tppt) REVERT: 8 42 ASP cc_start: 0.8502 (m-30) cc_final: 0.8086 (t70) REVERT: 8 82 SER cc_start: 0.9508 (m) cc_final: 0.9210 (p) REVERT: 9 51 GLU cc_start: 0.8331 (pt0) cc_final: 0.8129 (pt0) REVERT: 9 58 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8839 (mm-30) outliers start: 157 outliers final: 138 residues processed: 1006 average time/residue: 1.8427 time to fit residues: 3085.8657 Evaluate side-chains 1022 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 871 time to evaluate : 8.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 170 PHE Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 340 SER Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 445 ASP Chi-restraints excluded: chain M residue 452 TYR Chi-restraints excluded: chain M residue 469 ILE Chi-restraints excluded: chain M residue 640 LEU Chi-restraints excluded: chain M residue 644 LEU Chi-restraints excluded: chain M residue 645 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 300 TYR Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain N residue 465 LYS Chi-restraints excluded: chain N residue 488 ILE Chi-restraints excluded: chain N residue 546 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 640 LEU Chi-restraints excluded: chain N residue 641 GLU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 337 SER Chi-restraints excluded: chain O residue 347 SER Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 438 ILE Chi-restraints excluded: chain O residue 456 ASP Chi-restraints excluded: chain O residue 489 THR Chi-restraints excluded: chain O residue 553 VAL Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 640 LEU Chi-restraints excluded: chain P residue 183 GLU Chi-restraints excluded: chain P residue 304 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain P residue 582 ASP Chi-restraints excluded: chain P residue 622 ILE Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 31 TYR Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Y residue 275 THR Chi-restraints excluded: chain Y residue 340 SER Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 452 TYR Chi-restraints excluded: chain Y residue 482 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 644 LEU Chi-restraints excluded: chain Y residue 645 THR Chi-restraints excluded: chain Z residue 184 THR Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 331 SER Chi-restraints excluded: chain Z residue 351 ILE Chi-restraints excluded: chain Z residue 369 PHE Chi-restraints excluded: chain Z residue 439 THR Chi-restraints excluded: chain Z residue 465 LYS Chi-restraints excluded: chain Z residue 495 ASP Chi-restraints excluded: chain Z residue 601 LEU Chi-restraints excluded: chain Z residue 640 LEU Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 345 LYS Chi-restraints excluded: chain 0 residue 458 ILE Chi-restraints excluded: chain 0 residue 489 THR Chi-restraints excluded: chain 0 residue 601 LEU Chi-restraints excluded: chain 0 residue 640 LEU Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 265 VAL Chi-restraints excluded: chain 1 residue 275 THR Chi-restraints excluded: chain 1 residue 304 SER Chi-restraints excluded: chain 1 residue 347 SER Chi-restraints excluded: chain 1 residue 351 ILE Chi-restraints excluded: chain 1 residue 495 ASP Chi-restraints excluded: chain 1 residue 531 LEU Chi-restraints excluded: chain 1 residue 544 ASP Chi-restraints excluded: chain 1 residue 582 ASP Chi-restraints excluded: chain 1 residue 622 ILE Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 3 residue 42 ASP Chi-restraints excluded: chain 3 residue 67 ASP Chi-restraints excluded: chain 3 residue 94 THR Chi-restraints excluded: chain 3 residue 116 ASN Chi-restraints excluded: chain 4 residue 31 TYR Chi-restraints excluded: chain 4 residue 137 HIS Chi-restraints excluded: chain 4 residue 180 ARG Chi-restraints excluded: chain 5 residue 170 VAL Chi-restraints excluded: chain 6 residue 82 SER Chi-restraints excluded: chain 6 residue 85 ASP Chi-restraints excluded: chain 7 residue 30 GLN Chi-restraints excluded: chain 7 residue 47 ASN Chi-restraints excluded: chain 7 residue 86 GLN Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 67 SER Chi-restraints excluded: chain 9 residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 612 optimal weight: 20.0000 chunk 821 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 711 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 772 optimal weight: 0.7980 chunk 323 optimal weight: 10.0000 chunk 793 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN Z 192 GLN ** Z 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 594 GLN ** 5 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085831 restraints weight = 520224.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088736 restraints weight = 186861.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090344 restraints weight = 93789.685| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 77949 Z= 0.161 Angle : 0.545 9.576 106047 Z= 0.278 Chirality : 0.044 0.197 11823 Planarity : 0.004 0.116 13761 Dihedral : 5.458 53.404 10649 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.43 % Favored : 90.51 % Rotamer: Outliers : 1.44 % Allowed : 13.33 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.08), residues: 9759 helix: -0.14 (0.15), residues: 1260 sheet: -2.03 (0.10), residues: 2532 loop : -1.97 (0.08), residues: 5967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 356 HIS 0.006 0.001 HIS S 90 PHE 0.023 0.001 PHE Y 642 TYR 0.028 0.001 TYR L 89 ARG 0.016 0.000 ARG 3 147 =============================================================================== Job complete usr+sys time: 48916.28 seconds wall clock time: 840 minutes 47.86 seconds (50447.86 seconds total)