Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 27 02:55:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/10_2023/6gsi_0056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/10_2023/6gsi_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_0056/10_2023/6gsi_0056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/10_2023/6gsi_0056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/10_2023/6gsi_0056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsi_0056/10_2023/6gsi_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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 44.69, per 1000 atoms: 0.30 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: 91.28 Conformation dependent library (CDL) restraints added in 8.9 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: 5.14 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: 39.74 Time building geometry restraints manager: 96.55 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: 56405 16.16 - 32.32: 4309 32.32 - 48.48: 564 48.48 - 64.63: 66 64.63 - 80.79: 45 Dihedral angle restraints: 61389 sinusoidal: 27918 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 61386 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: 0.000 Normalize map: mean=0, sd=1: 10.390 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: 1.650 Extract box with map and model: 45.960 Check model and map are aligned: 1.610 Set scattering table: 0.990 Process input model: 343.720 Find NCS groups from input model: 7.130 Set up NCS constraints: 0.490 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: 0.020 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 413.770 ------------------------------------------------------------------------------- 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 *********************** 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 : 8.600 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 45 residues processed: 2109 average time/residue: 2.1135 time to fit residues: 7067.3036 Evaluate side-chains 1079 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1034 time to evaluate : 8.550 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 9 residues processed: 45 average time/residue: 1.5475 time to fit residues: 135.5714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 0.3980 chunk 736 optimal weight: 0.9980 chunk 408 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 496 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 761 optimal weight: 0.8980 chunk 294 optimal weight: 8.9990 chunk 463 optimal weight: 6.9990 chunk 567 optimal weight: 2.9990 chunk 882 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 I 54 ASN I 86 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 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 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 513 GLN P 378 ASN ** P 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 W 66 GLN 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 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** ** 1 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 190 ASN 5 90 HIS 5 190 ASN 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: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 77949 Z= 0.192 Angle : 0.652 8.094 106047 Z= 0.341 Chirality : 0.045 0.220 11823 Planarity : 0.005 0.085 13761 Dihedral : 6.760 37.153 10605 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.86 % Favored : 89.02 % Rotamer: Outliers : 1.46 % Allowed : 8.25 % Favored : 90.29 % 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: -4.24 (0.08), residues: 9759 helix: -2.51 (0.12), residues: 1224 sheet: -2.97 (0.09), residues: 2388 loop : -2.94 (0.07), residues: 6147 *********************** 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 1321 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1198 time to evaluate : 8.715 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 outliers start: 123 outliers final: 85 residues processed: 1286 average time/residue: 2.0146 time to fit residues: 4241.1121 Evaluate side-chains 1073 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 988 time to evaluate : 8.570 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 85 outliers final: 4 residues processed: 85 average time/residue: 1.5709 time to fit residues: 252.3669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 734 optimal weight: 0.9980 chunk 601 optimal weight: 3.9990 chunk 243 optimal weight: 0.5980 chunk 884 optimal weight: 8.9990 chunk 955 optimal weight: 8.9990 chunk 787 optimal weight: 7.9990 chunk 876 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 709 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 ASN ** 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 ** 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** ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 GLN 9 86 GLN 9 94 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 77949 Z= 0.275 Angle : 0.619 7.216 106047 Z= 0.322 Chirality : 0.044 0.186 11823 Planarity : 0.005 0.072 13761 Dihedral : 6.126 36.919 10605 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.70 % Favored : 88.18 % Rotamer: Outliers : 1.03 % Allowed : 9.65 % Favored : 89.32 % 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: -3.83 (0.08), residues: 9759 helix: -1.89 (0.13), residues: 1218 sheet: -2.77 (0.09), residues: 2499 loop : -2.68 (0.08), residues: 6042 *********************** 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 1154 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1067 time to evaluate : 8.675 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 outliers start: 87 outliers final: 63 residues processed: 1128 average time/residue: 1.9830 time to fit residues: 3691.7266 Evaluate side-chains 987 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 924 time to evaluate : 8.656 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 3 residues processed: 63 average time/residue: 1.4297 time to fit residues: 180.2844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 9.9990 chunk 664 optimal weight: 1.9990 chunk 458 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 422 optimal weight: 3.9990 chunk 593 optimal weight: 6.9990 chunk 887 optimal weight: 10.0000 chunk 939 optimal weight: 8.9990 chunk 463 optimal weight: 10.0000 chunk 841 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** F 190 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN L 86 GLN N 461 ASN N 463 ASN ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 594 GLN R 116 ASN R 190 ASN S 90 HIS ** T 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 HIS V 48 ASN V 49 GLN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 GLN ** X 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 474 GLN ** Z 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 192 GLN Z 461 ASN ** 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** 0 513 GLN ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN 6 86 GLN 7 54 ASN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 86 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 77949 Z= 0.348 Angle : 0.632 9.623 106047 Z= 0.329 Chirality : 0.045 0.176 11823 Planarity : 0.004 0.058 13761 Dihedral : 5.941 37.174 10605 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.40 % Favored : 87.47 % Rotamer: Outliers : 1.23 % Allowed : 10.72 % Favored : 88.05 % 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: -3.70 (0.08), residues: 9759 helix: -1.52 (0.14), residues: 1233 sheet: -2.70 (0.09), residues: 2553 loop : -2.64 (0.08), residues: 5973 *********************** 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 1046 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 942 time to evaluate : 8.723 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 outliers start: 104 outliers final: 77 residues processed: 1013 average time/residue: 1.9307 time to fit residues: 3217.5778 Evaluate side-chains 946 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 869 time to evaluate : 8.684 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 77 outliers final: 4 residues processed: 77 average time/residue: 1.4237 time to fit residues: 213.1333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 5.9990 chunk 533 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 699 optimal weight: 0.9980 chunk 387 optimal weight: 5.9990 chunk 801 optimal weight: 0.0060 chunk 649 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 479 optimal weight: 1.9990 chunk 843 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 474 GLN ** Z 178 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** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 30 GLN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 77949 Z= 0.181 Angle : 0.567 7.309 106047 Z= 0.291 Chirality : 0.044 0.180 11823 Planarity : 0.004 0.055 13761 Dihedral : 5.590 35.852 10605 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.91 % Favored : 90.00 % Rotamer: Outliers : 0.46 % Allowed : 11.46 % Favored : 88.08 % 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: -3.33 (0.08), residues: 9759 helix: -1.08 (0.14), residues: 1242 sheet: -2.55 (0.09), residues: 2499 loop : -2.38 (0.08), residues: 6018 *********************** 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 1012 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 973 time to evaluate : 8.816 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 outliers start: 39 outliers final: 22 residues processed: 996 average time/residue: 1.9342 time to fit residues: 3158.1032 Evaluate side-chains 925 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 903 time to evaluate : 8.608 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 22 average time/residue: 1.4598 time to fit residues: 69.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 316 optimal weight: 20.0000 chunk 846 optimal weight: 0.1980 chunk 185 optimal weight: 2.9990 chunk 551 optimal weight: 9.9990 chunk 231 optimal weight: 0.4980 chunk 940 optimal weight: 6.9990 chunk 780 optimal weight: 9.9990 chunk 435 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 493 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 V 30 GLN V 43 HIS V 44 GLN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 GLN Y 474 GLN ** 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** 6 86 GLN 7 54 ASN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 43 HIS 9 86 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 77949 Z= 0.182 Angle : 0.555 7.105 106047 Z= 0.284 Chirality : 0.044 0.163 11823 Planarity : 0.004 0.048 13761 Dihedral : 5.388 35.734 10605 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.55 % Favored : 89.33 % Rotamer: Outliers : 0.55 % Allowed : 11.98 % Favored : 87.48 % 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: -3.11 (0.08), residues: 9759 helix: -0.75 (0.15), residues: 1236 sheet: -2.38 (0.09), residues: 2511 loop : -2.29 (0.08), residues: 6012 *********************** 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 984 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 938 time to evaluate : 8.199 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 outliers start: 46 outliers final: 33 residues processed: 962 average time/residue: 1.9477 time to fit residues: 3076.0641 Evaluate side-chains 929 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 896 time to evaluate : 8.662 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 4 residues processed: 33 average time/residue: 1.5375 time to fit residues: 103.1269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 535 optimal weight: 8.9990 chunk 686 optimal weight: 0.8980 chunk 532 optimal weight: 8.9990 chunk 791 optimal weight: 6.9990 chunk 525 optimal weight: 7.9990 chunk 936 optimal weight: 10.0000 chunk 586 optimal weight: 5.9990 chunk 571 optimal weight: 0.0060 chunk 432 optimal weight: 3.9990 overall best weight: 3.3802 ------------------------------------------------------------------------------- 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 30 GLN ** J 48 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** Y 474 GLN ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 585 ASN ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 77949 Z= 0.235 Angle : 0.566 8.369 106047 Z= 0.290 Chirality : 0.044 0.174 11823 Planarity : 0.004 0.089 13761 Dihedral : 5.272 35.523 10605 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.12 % Favored : 88.79 % Rotamer: Outliers : 0.65 % Allowed : 11.95 % Favored : 87.39 % 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: -2.94 (0.08), residues: 9759 helix: -0.48 (0.15), residues: 1239 sheet: -2.31 (0.10), residues: 2511 loop : -2.17 (0.08), residues: 6009 *********************** 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 988 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 933 time to evaluate : 8.731 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 outliers start: 55 outliers final: 35 residues processed: 964 average time/residue: 1.9383 time to fit residues: 3074.6448 Evaluate side-chains 912 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 877 time to evaluate : 8.842 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 6 residues processed: 35 average time/residue: 1.4211 time to fit residues: 103.7745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 8.9990 chunk 374 optimal weight: 4.9990 chunk 559 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 595 optimal weight: 6.9990 chunk 638 optimal weight: 9.9990 chunk 463 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 736 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN ** L 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 GLN M 599 HIS ** N 484 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 HIS ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 372 ASN ** Z 513 GLN ** 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 ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 77949 Z= 0.400 Angle : 0.640 7.949 106047 Z= 0.334 Chirality : 0.046 0.187 11823 Planarity : 0.004 0.074 13761 Dihedral : 5.535 36.779 10605 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.98 % Favored : 85.93 % Rotamer: Outliers : 0.83 % Allowed : 12.48 % Favored : 86.69 % 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: -3.05 (0.08), residues: 9759 helix: -0.62 (0.15), residues: 1254 sheet: -2.29 (0.10), residues: 2523 loop : -2.29 (0.08), residues: 5982 *********************** 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 937 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 867 time to evaluate : 8.754 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 outliers start: 70 outliers final: 56 residues processed: 899 average time/residue: 1.9260 time to fit residues: 2841.9889 Evaluate side-chains 891 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 835 time to evaluate : 8.724 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 6 residues processed: 56 average time/residue: 1.4992 time to fit residues: 165.0908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 0.9980 chunk 897 optimal weight: 9.9990 chunk 818 optimal weight: 1.9990 chunk 873 optimal weight: 6.9990 chunk 525 optimal weight: 0.9990 chunk 380 optimal weight: 9.9990 chunk 685 optimal weight: 0.2980 chunk 267 optimal weight: 7.9990 chunk 788 optimal weight: 9.9990 chunk 825 optimal weight: 0.8980 chunk 869 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 463 ASN ** N 484 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 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 43 HIS ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 86 GLN ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5104 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= 0.158 Angle : 0.555 8.156 106047 Z= 0.283 Chirality : 0.044 0.238 11823 Planarity : 0.004 0.062 13761 Dihedral : 5.203 34.598 10605 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.36 % Favored : 90.58 % Rotamer: Outliers : 0.32 % Allowed : 12.74 % Favored : 86.94 % 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: -2.66 (0.08), residues: 9759 helix: -0.24 (0.15), residues: 1251 sheet: -2.12 (0.10), residues: 2475 loop : -2.01 (0.08), residues: 6033 *********************** 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 975 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 948 time to evaluate : 8.816 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 outliers start: 27 outliers final: 18 residues processed: 965 average time/residue: 1.8962 time to fit residues: 3019.3332 Evaluate side-chains 888 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 870 time to evaluate : 7.733 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 18 average time/residue: 1.4265 time to fit residues: 58.3327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 437 optimal weight: 6.9990 chunk 641 optimal weight: 9.9990 chunk 968 optimal weight: 4.9990 chunk 891 optimal weight: 7.9990 chunk 771 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 595 optimal weight: 9.9990 chunk 472 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 484 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 HIS ** 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 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** 1 594 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: 0.8255 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 77949 Z= 0.379 Angle : 0.618 8.154 106047 Z= 0.320 Chirality : 0.045 0.259 11823 Planarity : 0.004 0.071 13761 Dihedral : 5.338 36.176 10605 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.24 % Favored : 86.68 % Rotamer: Outliers : 0.38 % Allowed : 13.50 % Favored : 86.12 % 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: -2.81 (0.08), residues: 9759 helix: -0.25 (0.15), residues: 1230 sheet: -2.16 (0.10), residues: 2538 loop : -2.14 (0.08), residues: 5991 ********************** 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 891 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 859 time to evaluate : 8.873 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 outliers start: 32 outliers final: 29 residues processed: 874 average time/residue: 1.9073 time to fit residues: 2725.9719 Evaluate side-chains 867 residues out of total 8424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 838 time to evaluate : 8.724 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 6 residues processed: 29 average time/residue: 1.4770 time to fit residues: 89.8250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 612 optimal weight: 9.9990 chunk 821 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 711 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 chunk 772 optimal weight: 0.9990 chunk 323 optimal weight: 10.0000 chunk 793 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 GLN ** 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 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN N 484 ASN ** 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** ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 HIS V 47 ASN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 192 GLN ** Z 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 587 GLN ** 0 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.103494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084963 restraints weight = 523358.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087803 restraints weight = 188046.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089423 restraints weight = 95867.730| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 77949 Z= 0.189 Angle : 0.559 8.138 106047 Z= 0.285 Chirality : 0.044 0.219 11823 Planarity : 0.004 0.064 13761 Dihedral : 5.154 34.696 10605 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.95 % Favored : 89.99 % Rotamer: Outliers : 0.18 % Allowed : 13.78 % Favored : 86.04 % 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: -2.57 (0.08), residues: 9759 helix: -0.10 (0.15), residues: 1254 sheet: -2.05 (0.10), residues: 2496 loop : -1.96 (0.08), residues: 6009 =============================================================================== Job complete usr+sys time: 46111.61 seconds wall clock time: 792 minutes 2.54 seconds (47522.54 seconds total)