Starting phenix.real_space_refine on Tue Mar 19 08:14:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/03_2024/6ef1_9043_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/03_2024/6ef1_9043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/03_2024/6ef1_9043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/03_2024/6ef1_9043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/03_2024/6ef1_9043_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/03_2024/6ef1_9043_updated.pdb" } resolution = 4.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 66 5.16 5 C 14899 2.51 5 N 4080 2.21 5 O 4597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 266": "NH1" <-> "NH2" Residue "H PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 343": "NH1" <-> "NH2" Residue "J TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 212": "NH1" <-> "NH2" Residue "J ARG 228": "NH1" <-> "NH2" Residue "K ARG 259": "NH1" <-> "NH2" Residue "L ARG 342": "NH1" <-> "NH2" Residue "L PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23658 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1818 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 228} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1801 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1738 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 232} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1669 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ASN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "E" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1725 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 4, 'TRANS': 237} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 103 Chain: "F" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 226} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1822 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 233} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "H" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1764 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 13, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 117 Chain: "I" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1918 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 11, 'TRANS': 259} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "J" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 1923 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 12, 'TRANS': 260} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "K" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 1856 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 263} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 195 Chain: "L" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1867 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 249} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 109 Chain: "M" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1756 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 10, 'TRANS': 251} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 151 Chain: "s" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 87 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.76, per 1000 atoms: 0.54 Number of scatterers: 23658 At special positions: 0 Unit cell: (135.96, 140.08, 126.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 16 15.00 O 4597 8.00 N 4080 7.00 C 14899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 4.7 seconds 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 125 helices and 19 sheets defined 37.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.539A pdb=" N TYR A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 108 removed outlier: 3.684A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.730A pdb=" N GLN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 189 removed outlier: 4.065A pdb=" N THR A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.975A pdb=" N ILE A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.727A pdb=" N ARG A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 22 No H-bonds generated for 'chain 'B' and resid 19 through 22' Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.722A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 3.816A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 101 No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 107 through 118 removed outlier: 3.522A pdb=" N GLU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ILE B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 168 through 178 removed outlier: 4.045A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.948A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.638A pdb=" N ASN B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 31 removed outlier: 3.618A pdb=" N GLU C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 102 removed outlier: 4.117A pdb=" N ASN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 111 No H-bonds generated for 'chain 'C' and resid 108 through 111' Processing helix chain 'C' and resid 116 through 123 removed outlier: 4.107A pdb=" N GLN C 120 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 3.681A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 removed outlier: 4.669A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 232 through 242 removed outlier: 3.825A pdb=" N VAL C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 removed outlier: 4.240A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 99 removed outlier: 3.605A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.580A pdb=" N GLN D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.857A pdb=" N LEU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 203 removed outlier: 4.008A pdb=" N LEU D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 226 through 237 removed outlier: 3.601A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 82 through 102 removed outlier: 3.827A pdb=" N ARG E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 122 removed outlier: 3.622A pdb=" N GLN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU E 121 " --> pdb=" O CYS E 117 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 removed outlier: 4.943A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 204 removed outlier: 4.073A pdb=" N VAL E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 247 removed outlier: 3.948A pdb=" N ALA E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.985A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 98 removed outlier: 3.604A pdb=" N VAL F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER F 95 " --> pdb=" O GLN F 91 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.642A pdb=" N GLY F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.616A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 186 through 200 removed outlier: 3.509A pdb=" N ALA F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 232 removed outlier: 3.715A pdb=" N LYS F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 229 through 232' Processing helix chain 'G' and resid 22 through 33 removed outlier: 4.145A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 103 removed outlier: 4.076A pdb=" N LEU G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 116 Processing helix chain 'G' and resid 119 through 124 removed outlier: 3.508A pdb=" N THR G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 182 removed outlier: 3.812A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N HIS G 182 " --> pdb=" O LYS G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 207 removed outlier: 3.590A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA G 197 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 247 removed outlier: 4.339A pdb=" N LYS G 245 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 230 Proline residue: H 228 - end of helix Processing helix chain 'H' and resid 232 through 238 removed outlier: 3.910A pdb=" N LEU H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 267 removed outlier: 3.628A pdb=" N VAL H 263 " --> pdb=" O CYS H 259 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 279 No H-bonds generated for 'chain 'H' and resid 276 through 279' Processing helix chain 'H' and resid 286 through 298 removed outlier: 3.676A pdb=" N VAL H 291 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU H 293 " --> pdb=" O MET H 290 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU H 296 " --> pdb=" O GLU H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 343 removed outlier: 3.918A pdb=" N GLN H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 340 " --> pdb=" O LEU H 336 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY H 342 " --> pdb=" O THR H 338 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE H 343 " --> pdb=" O GLN H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 392 removed outlier: 3.885A pdb=" N ILE H 391 " --> pdb=" O ASN H 387 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS H 392 " --> pdb=" O ILE H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 Processing helix chain 'H' and resid 417 through 432 removed outlier: 4.196A pdb=" N THR H 424 " --> pdb=" O ARG H 420 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 452 removed outlier: 3.954A pdb=" N ALA H 446 " --> pdb=" O ASP H 442 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER H 452 " --> pdb=" O ASP H 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 171 No H-bonds generated for 'chain 'I' and resid 168 through 171' Processing helix chain 'I' and resid 189 through 197 Processing helix chain 'I' and resid 200 through 202 No H-bonds generated for 'chain 'I' and resid 200 through 202' Processing helix chain 'I' and resid 206 through 210 Processing helix chain 'I' and resid 231 through 239 Processing helix chain 'I' and resid 249 through 252 No H-bonds generated for 'chain 'I' and resid 249 through 252' Processing helix chain 'I' and resid 259 through 272 removed outlier: 3.556A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN I 266 " --> pdb=" O ARG I 262 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE I 267 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL I 270 " --> pdb=" O GLN I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 286 No H-bonds generated for 'chain 'I' and resid 284 through 286' Processing helix chain 'I' and resid 299 through 313 removed outlier: 4.132A pdb=" N MET I 306 " --> pdb=" O GLN I 303 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU I 307 " --> pdb=" O ARG I 304 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU I 310 " --> pdb=" O LEU I 307 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN I 311 " --> pdb=" O GLU I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 365 removed outlier: 3.756A pdb=" N ILE I 361 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU I 362 " --> pdb=" O LYS I 358 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY I 363 " --> pdb=" O LYS I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 404 removed outlier: 4.579A pdb=" N CYS I 396 " --> pdb=" O GLN I 393 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU I 398 " --> pdb=" O MET I 395 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA I 399 " --> pdb=" O CYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 426 removed outlier: 3.588A pdb=" N ALA I 419 " --> pdb=" O PHE I 416 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS I 420 " --> pdb=" O LYS I 417 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL I 423 " --> pdb=" O LYS I 420 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N MET I 424 " --> pdb=" O GLU I 421 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS I 425 " --> pdb=" O ARG I 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 169 removed outlier: 4.864A pdb=" N GLU J 162 " --> pdb=" O LYS J 158 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL J 163 " --> pdb=" O GLU J 159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Proline residue: J 167 - end of helix Processing helix chain 'J' and resid 171 through 177 removed outlier: 4.040A pdb=" N LEU J 177 " --> pdb=" O LEU J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 202 removed outlier: 3.844A pdb=" N ALA J 201 " --> pdb=" O LEU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 238 removed outlier: 3.771A pdb=" N MET J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 276 removed outlier: 3.606A pdb=" N GLN J 269 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG J 270 " --> pdb=" O GLU J 267 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET J 272 " --> pdb=" O GLN J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 287 Processing helix chain 'J' and resid 302 through 304 No H-bonds generated for 'chain 'J' and resid 302 through 304' Processing helix chain 'J' and resid 321 through 331 removed outlier: 4.016A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE J 330 " --> pdb=" O GLU J 326 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 347 removed outlier: 3.709A pdb=" N VAL J 346 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA J 347 " --> pdb=" O ARG J 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 343 through 347' Processing helix chain 'J' and resid 356 through 371 removed outlier: 3.675A pdb=" N GLU J 364 " --> pdb=" O GLY J 360 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET J 367 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR J 368 " --> pdb=" O GLU J 364 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA J 369 " --> pdb=" O ALA J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 392 removed outlier: 4.184A pdb=" N ALA J 385 " --> pdb=" O ASP J 381 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL J 386 " --> pdb=" O PHE J 382 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS J 388 " --> pdb=" O LEU J 384 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN J 391 " --> pdb=" O GLY J 387 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS J 392 " --> pdb=" O LYS J 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 185 removed outlier: 5.426A pdb=" N GLU K 183 " --> pdb=" O MET K 179 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 200 Processing helix chain 'K' and resid 219 through 222 No H-bonds generated for 'chain 'K' and resid 219 through 222' Processing helix chain 'K' and resid 227 through 229 No H-bonds generated for 'chain 'K' and resid 227 through 229' Processing helix chain 'K' and resid 249 through 263 removed outlier: 3.980A pdb=" N ARG K 255 " --> pdb=" O PRO K 251 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG K 259 " --> pdb=" O ARG K 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU K 263 " --> pdb=" O ARG K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 304 removed outlier: 3.707A pdb=" N GLU K 291 " --> pdb=" O GLY K 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL K 292 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 359 removed outlier: 3.672A pdb=" N ARG K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE K 356 " --> pdb=" O ILE K 352 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA K 357 " --> pdb=" O PHE K 353 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 373 No H-bonds generated for 'chain 'K' and resid 371 through 373' Processing helix chain 'K' and resid 382 through 392 removed outlier: 5.274A pdb=" N MET K 387 " --> pdb=" O ILE K 383 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU K 392 " --> pdb=" O GLN K 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 413 removed outlier: 3.663A pdb=" N GLU K 408 " --> pdb=" O GLN K 404 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU K 409 " --> pdb=" O SER K 405 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA K 410 " --> pdb=" O ASP K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 424 No H-bonds generated for 'chain 'K' and resid 421 through 424' Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 180 through 182 No H-bonds generated for 'chain 'L' and resid 180 through 182' Processing helix chain 'L' and resid 187 through 201 removed outlier: 3.853A pdb=" N ARG L 194 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 205 through 210 Processing helix chain 'L' and resid 228 through 239 removed outlier: 3.539A pdb=" N VAL L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE L 239 " --> pdb=" O VAL L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 271 removed outlier: 3.965A pdb=" N ALA L 260 " --> pdb=" O ILE L 256 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 283 through 285 No H-bonds generated for 'chain 'L' and resid 283 through 285' Processing helix chain 'L' and resid 297 through 313 removed outlier: 4.951A pdb=" N GLN L 302 " --> pdb=" O ARG L 299 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU L 308 " --> pdb=" O LEU L 305 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU L 309 " --> pdb=" O MET L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 338 Processing helix chain 'L' and resid 354 through 364 removed outlier: 4.634A pdb=" N GLU L 359 " --> pdb=" O ALA L 355 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE L 361 " --> pdb=" O ARG L 357 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS L 362 " --> pdb=" O LEU L 358 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) Processing helix chain 'L' and resid 375 through 381 removed outlier: 3.786A pdb=" N ALA L 378 " --> pdb=" O ASP L 375 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL L 380 " --> pdb=" O GLU L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 405 removed outlier: 4.118A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG L 404 " --> pdb=" O PHE L 400 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP L 405 " --> pdb=" O PHE L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 417 removed outlier: 3.944A pdb=" N MET L 416 " --> pdb=" O PRO L 412 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS L 417 " --> pdb=" O ASP L 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 412 through 417' Processing helix chain 'L' and resid 419 through 426 removed outlier: 3.549A pdb=" N ALA L 423 " --> pdb=" O VAL L 419 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 191 through 201 removed outlier: 3.625A pdb=" N GLU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU M 199 " --> pdb=" O GLU M 195 " (cutoff:3.500A) Proline residue: M 200 - end of helix Processing helix chain 'M' and resid 204 through 210 Processing helix chain 'M' and resid 228 through 233 Processing helix chain 'M' and resid 258 through 271 removed outlier: 3.535A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 286 No H-bonds generated for 'chain 'M' and resid 283 through 286' Processing helix chain 'M' and resid 301 through 317 Processing helix chain 'M' and resid 336 through 338 No H-bonds generated for 'chain 'M' and resid 336 through 338' Processing helix chain 'M' and resid 355 through 367 removed outlier: 3.692A pdb=" N LEU M 361 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN M 362 " --> pdb=" O ALA M 358 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS M 367 " --> pdb=" O ILE M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 382 Processing helix chain 'M' and resid 388 through 391 No H-bonds generated for 'chain 'M' and resid 388 through 391' Processing helix chain 'M' and resid 394 through 397 No H-bonds generated for 'chain 'M' and resid 394 through 397' Processing helix chain 'M' and resid 399 through 405 Processing helix chain 'M' and resid 416 through 420 Processing sheet with id= A, first strand: chain 'A' and resid 169 through 172 removed outlier: 6.242A pdb=" N ASN A 41 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 45 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 52 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR A 51 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 228 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 55 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 234 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 141 through 145 removed outlier: 3.703A pdb=" N LEU A 141 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.601A pdb=" N ALA B 46 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 43 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 212 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 236 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 135 through 137 removed outlier: 4.354A pdb=" N LEU B 147 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP B 159 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.566A pdb=" N LEU B 67 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.234A pdb=" N THR C 34 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 47 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 216 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 46 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA C 214 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= H, first strand: chain 'C' and resid 139 through 141 removed outlier: 4.148A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 141 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 161 through 163 removed outlier: 3.913A pdb=" N GLN D 162 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY D 35 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL D 43 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 42 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 213 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.524A pdb=" N VAL D 72 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 74 through 79 removed outlier: 3.507A pdb=" N GLY E 75 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 165 " --> pdb=" O HIS E 157 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 159 " --> pdb=" O THR E 163 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 220 through 223 removed outlier: 3.832A pdb=" N LYS E 229 " --> pdb=" O CYS E 221 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 37 through 39 removed outlier: 3.581A pdb=" N LEU F 38 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 214 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR F 223 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 153 through 156 removed outlier: 3.719A pdb=" N THR F 154 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU F 144 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE F 134 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 132 " --> pdb=" O PHE F 147 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY F 131 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP F 67 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 38 through 40 removed outlier: 4.203A pdb=" N GLY G 39 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA G 163 " --> pdb=" O GLY G 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 45 through 50 removed outlier: 4.112A pdb=" N GLU G 215 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 74 through 80 removed outlier: 3.500A pdb=" N GLY G 75 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 77 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 137 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER G 135 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY G 140 " --> pdb=" O HIS G 147 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 186 through 188 Processing sheet with id= S, first strand: chain 'M' and resid 219 through 221 597 hydrogen bonds defined for protein. 1578 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: 6.68 Time building geometry restraints manager: 10.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7952 1.34 - 1.46: 4983 1.46 - 1.58: 10974 1.58 - 1.70: 26 1.70 - 1.82: 106 Bond restraints: 24041 Sorted by residual: bond pdb=" C4 ATP J 501 " pdb=" C5 ATP J 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C4 ATP K 501 " pdb=" C5 ATP K 501 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.05e+01 bond pdb=" C4 ATP H 501 " pdb=" C5 ATP H 501 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" C5 ATP J 501 " pdb=" C6 ATP J 501 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.07e+01 ... (remaining 24036 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.97: 537 105.97 - 113.60: 13572 113.60 - 121.23: 11721 121.23 - 128.86: 6833 128.86 - 136.49: 138 Bond angle restraints: 32801 Sorted by residual: angle pdb=" PA ATP H 501 " pdb=" O3A ATP H 501 " pdb=" PB ATP H 501 " ideal model delta sigma weight residual 136.83 113.05 23.78 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PA ATP K 501 " pdb=" O3A ATP K 501 " pdb=" PB ATP K 501 " ideal model delta sigma weight residual 136.83 115.52 21.31 1.00e+00 1.00e+00 4.54e+02 angle pdb=" PB ATP K 501 " pdb=" O3B ATP K 501 " pdb=" PG ATP K 501 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.21e+02 angle pdb=" PB ATP H 501 " pdb=" O3B ATP H 501 " pdb=" PG ATP H 501 " ideal model delta sigma weight residual 139.87 120.85 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PB ATP I 501 " pdb=" O3B ATP I 501 " pdb=" PG ATP I 501 " ideal model delta sigma weight residual 139.87 123.53 16.34 1.00e+00 1.00e+00 2.67e+02 ... (remaining 32796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.49: 14071 26.49 - 52.98: 353 52.98 - 79.48: 43 79.48 - 105.97: 5 105.97 - 132.46: 1 Dihedral angle restraints: 14473 sinusoidal: 5004 harmonic: 9469 Sorted by residual: dihedral pdb=" O1B ADP L 501 " pdb=" O3A ADP L 501 " pdb=" PB ADP L 501 " pdb=" PA ADP L 501 " ideal model delta sinusoidal sigma weight residual 300.00 167.54 132.46 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" CA MET J 149 " pdb=" C MET J 149 " pdb=" N VAL J 150 " pdb=" CA VAL J 150 " ideal model delta harmonic sigma weight residual 180.00 -149.98 -30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ALA J 347 " pdb=" C ALA J 347 " pdb=" N GLU J 348 " pdb=" CA GLU J 348 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 14470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2519 0.044 - 0.088: 1054 0.088 - 0.132: 304 0.132 - 0.176: 51 0.176 - 0.220: 6 Chirality restraints: 3934 Sorted by residual: chirality pdb=" C2' ATP I 501 " pdb=" C1' ATP I 501 " pdb=" C3' ATP I 501 " pdb=" O2' ATP I 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C2' ATP H 501 " pdb=" C1' ATP H 501 " pdb=" C3' ATP H 501 " pdb=" O2' ATP H 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.49 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CG LEU L 415 " pdb=" CB LEU L 415 " pdb=" CD1 LEU L 415 " pdb=" CD2 LEU L 415 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 3931 not shown) Planarity restraints: 4254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 106 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 107 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 107 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 107 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER H 421 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C SER H 421 " 0.049 2.00e-02 2.50e+03 pdb=" O SER H 421 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL H 422 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 128 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO B 129 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.037 5.00e-02 4.00e+02 ... (remaining 4251 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 435 2.61 - 3.18: 24375 3.18 - 3.76: 34306 3.76 - 4.33: 47977 4.33 - 4.90: 71499 Nonbonded interactions: 178592 Sorted by model distance: nonbonded pdb=" O MET H 297 " pdb=" OG1 THR H 300 " model vdw 2.040 2.440 nonbonded pdb=" O ILE L 301 " pdb=" OG1 THR L 304 " model vdw 2.091 2.440 nonbonded pdb=" OG SER I 277 " pdb=" O ASP I 321 " model vdw 2.096 2.440 nonbonded pdb=" O ASN B 205 " pdb=" OG1 THR B 208 " model vdw 2.143 2.440 nonbonded pdb=" O GLU H 233 " pdb=" OG1 THR H 237 " model vdw 2.164 2.440 ... (remaining 178587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.110 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 63.160 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.009 0.100 24041 Z= 0.576 Angle : 0.988 23.775 32801 Z= 0.604 Chirality : 0.051 0.220 3934 Planarity : 0.006 0.083 4254 Dihedral : 12.317 132.459 8385 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.47 % Favored : 85.50 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.12), residues: 3262 helix: -3.99 (0.09), residues: 1014 sheet: -4.14 (0.19), residues: 356 loop : -3.07 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 187 HIS 0.014 0.003 HIS G 147 PHE 0.029 0.003 PHE E 123 TYR 0.024 0.003 TYR I 436 ARG 0.012 0.002 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 2.469 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: B 23 TYR cc_start: 0.8545 (m-10) cc_final: 0.8098 (m-80) REVERT: B 130 PHE cc_start: 0.8179 (m-80) cc_final: 0.7899 (m-80) REVERT: C 110 ILE cc_start: 0.8561 (mt) cc_final: 0.8256 (mm) REVERT: C 233 GLN cc_start: 0.8890 (pp30) cc_final: 0.8290 (pp30) REVERT: D 44 LEU cc_start: 0.8685 (mt) cc_final: 0.8472 (mm) REVERT: D 176 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8163 (mt-10) REVERT: D 230 ASN cc_start: 0.8072 (m110) cc_final: 0.7620 (m-40) REVERT: E 235 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7709 (mtpt) REVERT: F 73 SER cc_start: 0.8566 (p) cc_final: 0.8090 (m) REVERT: F 91 GLN cc_start: 0.9156 (mm110) cc_final: 0.8698 (tp40) REVERT: F 146 GLU cc_start: 0.7572 (tp30) cc_final: 0.7119 (tp30) REVERT: G 14 VAL cc_start: 0.8624 (t) cc_final: 0.8351 (m) REVERT: G 26 TYR cc_start: 0.8343 (m-10) cc_final: 0.8047 (m-80) REVERT: G 51 GLU cc_start: 0.8388 (tt0) cc_final: 0.7972 (tt0) REVERT: G 84 ASP cc_start: 0.8553 (t70) cc_final: 0.8212 (t0) REVERT: G 86 ARG cc_start: 0.7304 (ttt-90) cc_final: 0.6712 (ttt-90) REVERT: G 132 PHE cc_start: 0.8863 (m-10) cc_final: 0.8648 (m-10) REVERT: G 135 SER cc_start: 0.8911 (m) cc_final: 0.8628 (t) REVERT: H 304 CYS cc_start: 0.7433 (t) cc_final: 0.6819 (p) REVERT: H 310 GLU cc_start: 0.9141 (mp0) cc_final: 0.8570 (mp0) REVERT: H 356 ASN cc_start: 0.9309 (t160) cc_final: 0.9099 (t0) REVERT: I 254 GLN cc_start: 0.7680 (mp10) cc_final: 0.7264 (mp10) REVERT: I 255 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6193 (mmtm) REVERT: I 263 LEU cc_start: 0.9144 (mt) cc_final: 0.8943 (mt) REVERT: I 308 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7986 (mm-30) REVERT: J 204 HIS cc_start: 0.8063 (t70) cc_final: 0.7556 (t-90) REVERT: J 207 ASP cc_start: 0.8474 (m-30) cc_final: 0.8002 (t0) REVERT: J 236 MET cc_start: 0.8952 (tpt) cc_final: 0.8635 (tpp) REVERT: J 282 PHE cc_start: 0.9211 (p90) cc_final: 0.8912 (p90) REVERT: J 364 GLU cc_start: 0.9066 (tt0) cc_final: 0.8699 (tt0) REVERT: K 182 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8840 (tm-30) REVERT: L 191 ARG cc_start: 0.8987 (mtp180) cc_final: 0.8415 (mmm160) REVERT: L 199 LEU cc_start: 0.9198 (mm) cc_final: 0.8892 (mm) REVERT: L 317 ASN cc_start: 0.7993 (t0) cc_final: 0.7446 (p0) REVERT: L 362 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8907 (mmtp) REVERT: L 363 ILE cc_start: 0.8950 (pt) cc_final: 0.8629 (tt) REVERT: L 400 PHE cc_start: 0.7258 (m-10) cc_final: 0.6976 (m-80) REVERT: M 188 LYS cc_start: 0.7402 (mttt) cc_final: 0.7066 (tppt) REVERT: M 290 ARG cc_start: 0.5659 (pmt170) cc_final: 0.5430 (mtm180) REVERT: M 397 GLU cc_start: 0.8837 (mp0) cc_final: 0.8503 (mp0) REVERT: M 433 TYR cc_start: 0.8035 (m-10) cc_final: 0.7794 (m-10) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.3938 time to fit residues: 350.7175 Evaluate side-chains 366 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 30.0000 chunk 131 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 209 HIS B 41 ASN B 139 HIS C 125 HIS D 231 GLN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN F 86 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN H 392 HIS H 413 ASN I 312 GLN I 365 HIS I 418 GLN J 156 GLN ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 HIS ** K 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN M 412 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 24041 Z= 0.408 Angle : 0.812 9.612 32801 Z= 0.425 Chirality : 0.049 0.344 3934 Planarity : 0.006 0.071 4254 Dihedral : 9.870 110.225 3663 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.34 % Favored : 88.63 % Rotamer: Outliers : 0.27 % Allowed : 5.57 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.13), residues: 3262 helix: -2.82 (0.12), residues: 1167 sheet: -3.17 (0.22), residues: 400 loop : -2.98 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP H 404 HIS 0.011 0.002 HIS E 73 PHE 0.024 0.003 PHE H 343 TYR 0.026 0.002 TYR B 82 ARG 0.028 0.001 ARG M 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 473 time to evaluate : 2.659 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: A 130 GLN cc_start: 0.8053 (tt0) cc_final: 0.7583 (tt0) REVERT: A 212 ASP cc_start: 0.6831 (m-30) cc_final: 0.6349 (t0) REVERT: A 224 GLU cc_start: 0.7387 (tt0) cc_final: 0.7159 (tp30) REVERT: A 229 THR cc_start: 0.8768 (m) cc_final: 0.8503 (p) REVERT: B 5 TYR cc_start: 0.4626 (OUTLIER) cc_final: 0.3308 (m-80) REVERT: B 23 TYR cc_start: 0.8581 (m-10) cc_final: 0.8278 (m-10) REVERT: B 134 LEU cc_start: 0.8750 (pp) cc_final: 0.8387 (pp) REVERT: C 242 THR cc_start: 0.9159 (m) cc_final: 0.8903 (t) REVERT: D 111 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.6975 (mtm-85) REVERT: E 166 ARG cc_start: 0.8464 (ttt90) cc_final: 0.7989 (tpt-90) REVERT: F 137 TYR cc_start: 0.7818 (t80) cc_final: 0.7542 (t80) REVERT: G 26 TYR cc_start: 0.8427 (m-10) cc_final: 0.8212 (m-10) REVERT: G 84 ASP cc_start: 0.8796 (t70) cc_final: 0.8398 (t0) REVERT: G 135 SER cc_start: 0.8585 (m) cc_final: 0.8038 (t) REVERT: H 210 ASP cc_start: 0.8498 (m-30) cc_final: 0.8201 (m-30) REVERT: H 310 GLU cc_start: 0.9146 (mp0) cc_final: 0.8619 (mp0) REVERT: I 192 GLN cc_start: 0.9482 (pt0) cc_final: 0.9189 (pm20) REVERT: I 208 TYR cc_start: 0.8438 (m-80) cc_final: 0.8122 (m-80) REVERT: I 254 GLN cc_start: 0.7933 (mp10) cc_final: 0.7505 (mp10) REVERT: I 255 LYS cc_start: 0.7429 (mmtm) cc_final: 0.6431 (mmtm) REVERT: I 304 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8403 (ttm110) REVERT: J 149 MET cc_start: 0.8645 (tpp) cc_final: 0.8281 (tpp) REVERT: J 282 PHE cc_start: 0.9131 (p90) cc_final: 0.8730 (p90) REVERT: J 367 MET cc_start: 0.9480 (mtp) cc_final: 0.9183 (mtp) REVERT: K 168 ASP cc_start: 0.8545 (p0) cc_final: 0.8262 (m-30) REVERT: K 304 ASP cc_start: 0.9450 (t70) cc_final: 0.9057 (t0) REVERT: L 191 ARG cc_start: 0.9112 (mtp180) cc_final: 0.8901 (mtp180) REVERT: L 194 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7164 (ttp-110) REVERT: L 317 ASN cc_start: 0.8039 (t0) cc_final: 0.7346 (p0) REVERT: L 362 LYS cc_start: 0.9230 (mmtm) cc_final: 0.8878 (mmtp) REVERT: L 416 MET cc_start: 0.9043 (mmt) cc_final: 0.8538 (mmm) REVERT: M 188 LYS cc_start: 0.7021 (mttt) cc_final: 0.6316 (tppt) REVERT: M 290 ARG cc_start: 0.5779 (pmt170) cc_final: 0.5374 (mtm180) REVERT: M 343 LEU cc_start: 0.8402 (tt) cc_final: 0.8183 (mm) outliers start: 6 outliers final: 0 residues processed: 478 average time/residue: 0.3425 time to fit residues: 258.3597 Evaluate side-chains 344 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 0.0170 chunk 244 optimal weight: 30.0000 chunk 200 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 0.0770 chunk 318 optimal weight: 20.0000 chunk 262 optimal weight: 0.1980 chunk 292 optimal weight: 7.9990 chunk 100 optimal weight: 0.0270 chunk 236 optimal weight: 5.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 176 GLN B 41 ASN C 120 GLN D 230 ASN E 23 GLN E 91 HIS F 100 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN I 312 GLN J 240 HIS K 228 ASN K 293 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 24041 Z= 0.167 Angle : 0.656 8.732 32801 Z= 0.329 Chirality : 0.045 0.169 3934 Planarity : 0.004 0.055 4254 Dihedral : 8.742 107.589 3663 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.65 % Favored : 93.32 % Rotamer: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.14), residues: 3262 helix: -2.01 (0.13), residues: 1200 sheet: -2.69 (0.22), residues: 443 loop : -2.47 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 404 HIS 0.010 0.001 HIS J 240 PHE 0.019 0.002 PHE L 207 TYR 0.032 0.001 TYR A 30 ARG 0.008 0.001 ARG M 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 506 time to evaluate : 2.653 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: A 42 SER cc_start: 0.8936 (p) cc_final: 0.8359 (m) REVERT: A 55 SER cc_start: 0.7974 (p) cc_final: 0.7196 (p) REVERT: A 65 ASP cc_start: 0.7275 (m-30) cc_final: 0.6902 (m-30) REVERT: A 126 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 130 GLN cc_start: 0.7811 (tt0) cc_final: 0.7348 (tt0) REVERT: A 175 GLN cc_start: 0.7384 (pp30) cc_final: 0.7170 (pp30) REVERT: B 23 TYR cc_start: 0.8554 (m-10) cc_final: 0.8205 (m-80) REVERT: B 35 LEU cc_start: 0.9008 (pt) cc_final: 0.8760 (pt) REVERT: B 65 SER cc_start: 0.8845 (m) cc_final: 0.8621 (p) REVERT: B 75 TYR cc_start: 0.8328 (p90) cc_final: 0.6650 (p90) REVERT: B 82 TYR cc_start: 0.8760 (t80) cc_final: 0.7903 (t80) REVERT: B 87 ASP cc_start: 0.8635 (m-30) cc_final: 0.8359 (m-30) REVERT: B 134 LEU cc_start: 0.8636 (pp) cc_final: 0.7966 (pp) REVERT: C 12 ILE cc_start: 0.7532 (tp) cc_final: 0.7028 (pt) REVERT: C 163 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8523 (mm) REVERT: C 242 THR cc_start: 0.9156 (m) cc_final: 0.8885 (t) REVERT: D 111 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.6928 (mtm-85) REVERT: E 183 LEU cc_start: 0.9498 (mt) cc_final: 0.9269 (mm) REVERT: F 73 SER cc_start: 0.8887 (p) cc_final: 0.8209 (m) REVERT: F 117 GLN cc_start: 0.8316 (mm110) cc_final: 0.7863 (mm-40) REVERT: G 84 ASP cc_start: 0.8816 (t70) cc_final: 0.7959 (t0) REVERT: G 135 SER cc_start: 0.8185 (m) cc_final: 0.7635 (t) REVERT: G 144 ASN cc_start: 0.8735 (t0) cc_final: 0.8484 (t0) REVERT: G 204 HIS cc_start: 0.7550 (t70) cc_final: 0.7247 (t70) REVERT: H 210 ASP cc_start: 0.8489 (m-30) cc_final: 0.8230 (m-30) REVERT: H 310 GLU cc_start: 0.8985 (mp0) cc_final: 0.8480 (mp0) REVERT: H 328 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7953 (mm-30) REVERT: I 208 TYR cc_start: 0.8195 (m-80) cc_final: 0.7870 (m-80) REVERT: I 254 GLN cc_start: 0.7829 (mp10) cc_final: 0.7448 (mp10) REVERT: I 304 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8385 (ttm110) REVERT: J 149 MET cc_start: 0.8424 (tpp) cc_final: 0.8134 (tpp) REVERT: J 210 PHE cc_start: 0.8242 (t80) cc_final: 0.8023 (t80) REVERT: J 282 PHE cc_start: 0.9034 (p90) cc_final: 0.8653 (p90) REVERT: J 364 GLU cc_start: 0.9081 (tt0) cc_final: 0.8752 (mm-30) REVERT: J 367 MET cc_start: 0.9350 (mtp) cc_final: 0.8328 (mtp) REVERT: K 178 ASP cc_start: 0.8798 (p0) cc_final: 0.8547 (p0) REVERT: K 304 ASP cc_start: 0.9495 (t70) cc_final: 0.8877 (t0) REVERT: L 191 ARG cc_start: 0.9052 (mtp180) cc_final: 0.8814 (mtp180) REVERT: L 194 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7449 (ttp-110) REVERT: L 219 LEU cc_start: 0.8744 (pt) cc_final: 0.8458 (pp) REVERT: L 266 MET cc_start: 0.9572 (ttp) cc_final: 0.9237 (ppp) REVERT: L 353 ASN cc_start: 0.8609 (t0) cc_final: 0.8375 (p0) REVERT: L 397 GLU cc_start: 0.8662 (pp20) cc_final: 0.8454 (pt0) REVERT: M 188 LYS cc_start: 0.7083 (mttt) cc_final: 0.6531 (tppt) REVERT: M 387 ASN cc_start: 0.8904 (p0) cc_final: 0.8229 (p0) REVERT: M 419 ILE cc_start: 0.8698 (mt) cc_final: 0.8494 (mm) outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.3352 time to fit residues: 264.1674 Evaluate side-chains 365 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 140 optimal weight: 0.0570 chunk 197 optimal weight: 10.0000 chunk 295 optimal weight: 0.9990 chunk 313 optimal weight: 50.0000 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 84 optimal weight: 0.0270 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 176 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN I 426 ASN J 240 HIS ** L 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24041 Z= 0.169 Angle : 0.612 9.457 32801 Z= 0.308 Chirality : 0.044 0.214 3934 Planarity : 0.004 0.053 4254 Dihedral : 8.248 105.660 3663 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.14), residues: 3262 helix: -1.51 (0.14), residues: 1194 sheet: -2.20 (0.23), residues: 450 loop : -2.24 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 404 HIS 0.008 0.001 HIS J 240 PHE 0.028 0.002 PHE H 343 TYR 0.018 0.001 TYR L 221 ARG 0.005 0.000 ARG H 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 469 time to evaluate : 2.783 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: A 42 SER cc_start: 0.8848 (p) cc_final: 0.8398 (m) REVERT: A 55 SER cc_start: 0.7759 (p) cc_final: 0.7367 (p) REVERT: A 130 GLN cc_start: 0.7853 (tt0) cc_final: 0.7375 (tt0) REVERT: B 23 TYR cc_start: 0.8528 (m-10) cc_final: 0.8244 (m-10) REVERT: B 65 SER cc_start: 0.8832 (m) cc_final: 0.8485 (p) REVERT: B 75 TYR cc_start: 0.8402 (p90) cc_final: 0.6833 (p90) REVERT: B 134 LEU cc_start: 0.8656 (pp) cc_final: 0.8077 (pp) REVERT: C 12 ILE cc_start: 0.7573 (tp) cc_final: 0.7115 (pt) REVERT: C 73 ILE cc_start: 0.7679 (mt) cc_final: 0.7478 (mt) REVERT: C 237 ASP cc_start: 0.8889 (p0) cc_final: 0.8673 (p0) REVERT: C 242 THR cc_start: 0.9136 (m) cc_final: 0.8844 (t) REVERT: E 50 VAL cc_start: 0.8739 (m) cc_final: 0.8512 (p) REVERT: G 74 ILE cc_start: 0.8541 (mt) cc_final: 0.8150 (mm) REVERT: G 84 ASP cc_start: 0.8831 (t70) cc_final: 0.8333 (t0) REVERT: H 210 ASP cc_start: 0.8674 (m-30) cc_final: 0.8460 (m-30) REVERT: H 356 ASN cc_start: 0.9408 (t0) cc_final: 0.9190 (t0) REVERT: H 448 ASP cc_start: 0.8474 (t0) cc_final: 0.8106 (t0) REVERT: I 196 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8658 (mt-10) REVERT: I 208 TYR cc_start: 0.8155 (m-80) cc_final: 0.7895 (m-80) REVERT: I 254 GLN cc_start: 0.7865 (mp10) cc_final: 0.7471 (mp10) REVERT: I 304 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8393 (ttm110) REVERT: I 383 THR cc_start: 0.8734 (m) cc_final: 0.8460 (p) REVERT: J 149 MET cc_start: 0.8740 (tpp) cc_final: 0.8463 (tpp) REVERT: J 282 PHE cc_start: 0.9039 (p90) cc_final: 0.8667 (p90) REVERT: J 364 GLU cc_start: 0.9161 (tt0) cc_final: 0.8849 (mm-30) REVERT: J 367 MET cc_start: 0.9366 (mtp) cc_final: 0.8483 (mtp) REVERT: K 178 ASP cc_start: 0.8870 (p0) cc_final: 0.8617 (p0) REVERT: K 304 ASP cc_start: 0.9582 (t70) cc_final: 0.8977 (t0) REVERT: K 393 ARG cc_start: 0.7572 (mmp80) cc_final: 0.7329 (mmm160) REVERT: L 191 ARG cc_start: 0.9069 (mtp180) cc_final: 0.8842 (ptm160) REVERT: L 194 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7462 (ttp-110) REVERT: L 266 MET cc_start: 0.9580 (ttp) cc_final: 0.9279 (ppp) REVERT: L 282 GLU cc_start: 0.8098 (tp30) cc_final: 0.7863 (tp30) REVERT: L 353 ASN cc_start: 0.8718 (t0) cc_final: 0.8457 (p0) REVERT: L 394 CYS cc_start: 0.9189 (t) cc_final: 0.8735 (t) REVERT: L 397 GLU cc_start: 0.8681 (pp20) cc_final: 0.8397 (pp20) REVERT: M 188 LYS cc_start: 0.7177 (mttt) cc_final: 0.6518 (tppt) REVERT: M 377 GLN cc_start: 0.8436 (mp10) cc_final: 0.8111 (mp10) REVERT: M 390 GLN cc_start: 0.8521 (mp10) cc_final: 0.8238 (mp10) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.3211 time to fit residues: 240.5607 Evaluate side-chains 363 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 233 optimal weight: 0.0060 chunk 129 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 216 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN D 117 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN K 194 GLN K 264 ASN L 273 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 24041 Z= 0.396 Angle : 0.757 9.583 32801 Z= 0.391 Chirality : 0.047 0.231 3934 Planarity : 0.005 0.060 4254 Dihedral : 8.639 106.662 3663 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.14), residues: 3262 helix: -1.64 (0.14), residues: 1227 sheet: -2.09 (0.23), residues: 445 loop : -2.40 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 160 HIS 0.011 0.002 HIS J 205 PHE 0.041 0.003 PHE D 18 TYR 0.024 0.002 TYR L 221 ARG 0.019 0.001 ARG H 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 2.715 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: A 126 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 221 ASN cc_start: 0.8417 (p0) cc_final: 0.8109 (p0) REVERT: A 229 THR cc_start: 0.8711 (m) cc_final: 0.8446 (p) REVERT: C 12 ILE cc_start: 0.7516 (tp) cc_final: 0.6850 (pt) REVERT: C 237 ASP cc_start: 0.8967 (p0) cc_final: 0.8762 (p0) REVERT: D 111 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.6859 (mtm-85) REVERT: D 133 THR cc_start: 0.7957 (p) cc_final: 0.7730 (t) REVERT: E 180 GLN cc_start: 0.7965 (pm20) cc_final: 0.7701 (pm20) REVERT: F 117 GLN cc_start: 0.8176 (mm110) cc_final: 0.7704 (tp40) REVERT: G 74 ILE cc_start: 0.8745 (mt) cc_final: 0.8404 (mm) REVERT: G 84 ASP cc_start: 0.8721 (t70) cc_final: 0.8218 (t0) REVERT: G 94 GLU cc_start: 0.8919 (pp20) cc_final: 0.8613 (pp20) REVERT: G 121 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7822 (tm-30) REVERT: H 210 ASP cc_start: 0.8782 (m-30) cc_final: 0.8554 (m-30) REVERT: H 249 TYR cc_start: 0.8312 (p90) cc_final: 0.8084 (p90) REVERT: H 310 GLU cc_start: 0.9150 (mp0) cc_final: 0.8674 (mp0) REVERT: H 356 ASN cc_start: 0.9465 (t0) cc_final: 0.9260 (t0) REVERT: I 208 TYR cc_start: 0.8448 (m-80) cc_final: 0.8243 (m-80) REVERT: I 304 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8333 (ttm110) REVERT: I 326 MET cc_start: 0.7045 (tpt) cc_final: 0.6823 (tpt) REVERT: I 383 THR cc_start: 0.8908 (m) cc_final: 0.8657 (p) REVERT: J 149 MET cc_start: 0.8899 (tpp) cc_final: 0.8442 (tpp) REVERT: J 265 ASP cc_start: 0.8881 (p0) cc_final: 0.8592 (p0) REVERT: J 282 PHE cc_start: 0.9104 (p90) cc_final: 0.8762 (p90) REVERT: J 364 GLU cc_start: 0.9187 (tt0) cc_final: 0.8907 (mm-30) REVERT: J 367 MET cc_start: 0.9389 (mtp) cc_final: 0.8423 (mtp) REVERT: K 194 GLN cc_start: 0.9085 (mp10) cc_final: 0.8633 (mp10) REVERT: L 191 ARG cc_start: 0.9135 (mtp180) cc_final: 0.8730 (mtp180) REVERT: L 194 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7221 (ttp-110) REVERT: L 263 ILE cc_start: 0.9252 (pt) cc_final: 0.8874 (pt) REVERT: L 266 MET cc_start: 0.9641 (ttp) cc_final: 0.9210 (tmm) REVERT: L 282 GLU cc_start: 0.8124 (tp30) cc_final: 0.7890 (tp30) REVERT: L 394 CYS cc_start: 0.9360 (t) cc_final: 0.8956 (t) REVERT: L 397 GLU cc_start: 0.8738 (pp20) cc_final: 0.8359 (pp20) REVERT: L 400 PHE cc_start: 0.7543 (m-10) cc_final: 0.7222 (m-10) REVERT: M 188 LYS cc_start: 0.7243 (mttt) cc_final: 0.6452 (tppt) REVERT: M 203 ARG cc_start: 0.9321 (mmm160) cc_final: 0.9084 (tpp-160) REVERT: M 290 ARG cc_start: 0.5726 (pmt170) cc_final: 0.5098 (mtm180) REVERT: M 390 GLN cc_start: 0.8594 (mp10) cc_final: 0.8323 (mp10) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.3163 time to fit residues: 212.1133 Evaluate side-chains 340 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 6.9990 chunk 282 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 313 optimal weight: 40.0000 chunk 260 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN E 114 GLN E 185 ASN ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN I 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24041 Z= 0.262 Angle : 0.655 8.604 32801 Z= 0.334 Chirality : 0.045 0.241 3934 Planarity : 0.004 0.068 4254 Dihedral : 8.222 103.270 3663 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.14), residues: 3262 helix: -1.40 (0.14), residues: 1236 sheet: -1.88 (0.23), residues: 451 loop : -2.27 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 159 HIS 0.011 0.001 HIS G 204 PHE 0.031 0.002 PHE H 343 TYR 0.022 0.002 TYR L 221 ARG 0.006 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 2.598 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: A 126 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8254 (tm-30) REVERT: A 221 ASN cc_start: 0.8430 (p0) cc_final: 0.8106 (p0) REVERT: A 229 THR cc_start: 0.8651 (m) cc_final: 0.8409 (p) REVERT: C 12 ILE cc_start: 0.7632 (tp) cc_final: 0.7037 (pt) REVERT: C 237 ASP cc_start: 0.8958 (p0) cc_final: 0.8736 (p0) REVERT: D 111 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.6882 (mtm-85) REVERT: F 117 GLN cc_start: 0.8034 (mm110) cc_final: 0.7634 (tp40) REVERT: G 84 ASP cc_start: 0.8616 (t70) cc_final: 0.8042 (t0) REVERT: G 94 GLU cc_start: 0.8830 (pp20) cc_final: 0.8531 (pp20) REVERT: G 121 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7776 (tm-30) REVERT: G 204 HIS cc_start: 0.8002 (t70) cc_final: 0.7752 (t70) REVERT: H 249 TYR cc_start: 0.8181 (p90) cc_final: 0.7956 (p90) REVERT: H 310 GLU cc_start: 0.9116 (mp0) cc_final: 0.8658 (mp0) REVERT: H 356 ASN cc_start: 0.9465 (t0) cc_final: 0.9247 (t0) REVERT: H 399 GLU cc_start: 0.9185 (tt0) cc_final: 0.8546 (tm-30) REVERT: I 208 TYR cc_start: 0.8416 (m-80) cc_final: 0.8096 (m-80) REVERT: I 255 LYS cc_start: 0.7573 (mmtm) cc_final: 0.6483 (mmtm) REVERT: I 304 ARG cc_start: 0.8801 (ttm110) cc_final: 0.8395 (ttm110) REVERT: I 308 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6243 (mm-30) REVERT: I 326 MET cc_start: 0.6871 (tpt) cc_final: 0.6615 (tpt) REVERT: I 380 LEU cc_start: 0.8983 (mp) cc_final: 0.8747 (mp) REVERT: I 383 THR cc_start: 0.8911 (m) cc_final: 0.8674 (p) REVERT: J 149 MET cc_start: 0.8835 (tpp) cc_final: 0.8313 (tpp) REVERT: J 265 ASP cc_start: 0.8912 (p0) cc_final: 0.8629 (p0) REVERT: J 282 PHE cc_start: 0.9083 (p90) cc_final: 0.8719 (p90) REVERT: J 357 ASP cc_start: 0.8642 (p0) cc_final: 0.8412 (p0) REVERT: J 364 GLU cc_start: 0.9154 (tt0) cc_final: 0.8898 (mm-30) REVERT: K 178 ASP cc_start: 0.9025 (p0) cc_final: 0.8739 (p0) REVERT: K 194 GLN cc_start: 0.9000 (mp10) cc_final: 0.8619 (mp10) REVERT: L 191 ARG cc_start: 0.9110 (mtp180) cc_final: 0.8743 (mtp180) REVERT: L 194 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7312 (ttp-110) REVERT: L 199 LEU cc_start: 0.9376 (mp) cc_final: 0.8866 (mp) REVERT: L 266 MET cc_start: 0.9605 (ttp) cc_final: 0.9301 (ppp) REVERT: L 282 GLU cc_start: 0.8106 (tp30) cc_final: 0.7883 (tp30) REVERT: L 394 CYS cc_start: 0.9286 (t) cc_final: 0.8778 (t) REVERT: L 397 GLU cc_start: 0.8653 (pp20) cc_final: 0.8229 (pp20) REVERT: L 400 PHE cc_start: 0.7461 (m-10) cc_final: 0.7136 (m-10) REVERT: M 188 LYS cc_start: 0.7241 (mttt) cc_final: 0.6410 (tppt) REVERT: M 203 ARG cc_start: 0.9328 (mmm160) cc_final: 0.9108 (tpp-160) REVERT: M 368 MET cc_start: 0.7092 (tpp) cc_final: 0.6816 (mmt) REVERT: M 390 GLN cc_start: 0.8930 (mp10) cc_final: 0.8398 (mp10) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.3220 time to fit residues: 221.7614 Evaluate side-chains 338 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 312 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN I 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 24041 Z= 0.403 Angle : 0.762 9.252 32801 Z= 0.393 Chirality : 0.048 0.255 3934 Planarity : 0.005 0.060 4254 Dihedral : 8.499 104.507 3663 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.14), residues: 3262 helix: -1.52 (0.14), residues: 1231 sheet: -1.91 (0.23), residues: 455 loop : -2.31 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 159 HIS 0.009 0.002 HIS J 240 PHE 0.032 0.003 PHE D 18 TYR 0.028 0.002 TYR B 82 ARG 0.007 0.001 ARG I 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 428 time to evaluate : 2.949 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: A 221 ASN cc_start: 0.8461 (p0) cc_final: 0.8173 (p0) REVERT: A 229 THR cc_start: 0.8747 (m) cc_final: 0.8457 (p) REVERT: C 80 LEU cc_start: 0.8892 (mm) cc_final: 0.8671 (tp) REVERT: C 233 GLN cc_start: 0.8715 (pt0) cc_final: 0.8477 (pt0) REVERT: D 88 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8312 (mtmm) REVERT: D 111 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.6870 (mtm-85) REVERT: F 137 TYR cc_start: 0.7763 (t80) cc_final: 0.7538 (t80) REVERT: G 26 TYR cc_start: 0.8476 (m-80) cc_final: 0.8195 (m-10) REVERT: G 33 ASN cc_start: 0.8849 (m-40) cc_final: 0.8568 (m110) REVERT: H 249 TYR cc_start: 0.8439 (p90) cc_final: 0.8177 (p90) REVERT: H 310 GLU cc_start: 0.9149 (mp0) cc_final: 0.8729 (mp0) REVERT: H 356 ASN cc_start: 0.9500 (t0) cc_final: 0.9293 (t0) REVERT: H 399 GLU cc_start: 0.9242 (tt0) cc_final: 0.8621 (tm-30) REVERT: I 208 TYR cc_start: 0.8524 (m-80) cc_final: 0.8212 (m-80) REVERT: I 326 MET cc_start: 0.6815 (tpt) cc_final: 0.6561 (tpt) REVERT: I 383 THR cc_start: 0.8879 (m) cc_final: 0.8664 (p) REVERT: J 149 MET cc_start: 0.8916 (tpp) cc_final: 0.8413 (tpp) REVERT: J 265 ASP cc_start: 0.8940 (p0) cc_final: 0.8687 (p0) REVERT: J 282 PHE cc_start: 0.9121 (p90) cc_final: 0.8798 (p90) REVERT: J 364 GLU cc_start: 0.9257 (tt0) cc_final: 0.8894 (tp30) REVERT: K 178 ASP cc_start: 0.9081 (p0) cc_final: 0.8790 (p0) REVERT: K 194 GLN cc_start: 0.9068 (mp10) cc_final: 0.8645 (mp10) REVERT: L 191 ARG cc_start: 0.9076 (mtp180) cc_final: 0.8829 (mtp180) REVERT: L 194 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7251 (ttp-110) REVERT: L 263 ILE cc_start: 0.9243 (pt) cc_final: 0.8966 (pt) REVERT: L 266 MET cc_start: 0.9627 (ttp) cc_final: 0.9174 (tmm) REVERT: L 279 PHE cc_start: 0.8848 (t80) cc_final: 0.8563 (t80) REVERT: L 282 GLU cc_start: 0.8116 (tp30) cc_final: 0.7897 (tp30) REVERT: L 397 GLU cc_start: 0.8754 (pp20) cc_final: 0.8363 (pp20) REVERT: L 400 PHE cc_start: 0.7510 (m-10) cc_final: 0.7173 (m-10) REVERT: M 188 LYS cc_start: 0.7126 (mttt) cc_final: 0.6298 (tppt) REVERT: M 203 ARG cc_start: 0.9315 (mmm160) cc_final: 0.9104 (tpp-160) REVERT: M 290 ARG cc_start: 0.5896 (pmt170) cc_final: 0.5432 (mtm180) REVERT: M 390 GLN cc_start: 0.8953 (mp10) cc_final: 0.8360 (mp10) REVERT: M 411 LYS cc_start: 0.8374 (ttmm) cc_final: 0.7929 (tptt) outliers start: 2 outliers final: 1 residues processed: 430 average time/residue: 0.3264 time to fit residues: 222.6705 Evaluate side-chains 332 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 331 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN D 117 GLN F 5 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 170 GLN I 312 GLN J 204 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24041 Z= 0.290 Angle : 0.686 9.251 32801 Z= 0.350 Chirality : 0.046 0.236 3934 Planarity : 0.004 0.060 4254 Dihedral : 8.166 102.473 3663 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.14), residues: 3262 helix: -1.34 (0.14), residues: 1215 sheet: -1.78 (0.22), residues: 461 loop : -2.16 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 404 HIS 0.008 0.001 HIS G 73 PHE 0.035 0.002 PHE H 343 TYR 0.024 0.002 TYR B 82 ARG 0.005 0.001 ARG I 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 2.973 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: A 221 ASN cc_start: 0.8551 (p0) cc_final: 0.8216 (p0) REVERT: A 229 THR cc_start: 0.8729 (m) cc_final: 0.8462 (p) REVERT: C 26 LEU cc_start: 0.8662 (pt) cc_final: 0.8428 (pt) REVERT: C 80 LEU cc_start: 0.8894 (mm) cc_final: 0.8689 (tp) REVERT: D 111 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.6914 (mtm-85) REVERT: E 180 GLN cc_start: 0.7839 (pm20) cc_final: 0.7616 (pm20) REVERT: F 137 TYR cc_start: 0.7797 (t80) cc_final: 0.7594 (t80) REVERT: G 33 ASN cc_start: 0.8831 (m-40) cc_final: 0.8526 (m110) REVERT: G 38 ILE cc_start: 0.8889 (pt) cc_final: 0.8436 (mp) REVERT: H 249 TYR cc_start: 0.8434 (p90) cc_final: 0.8160 (p90) REVERT: H 310 GLU cc_start: 0.9099 (mp0) cc_final: 0.8679 (mp0) REVERT: H 356 ASN cc_start: 0.9512 (t0) cc_final: 0.9268 (t0) REVERT: I 208 TYR cc_start: 0.8523 (m-80) cc_final: 0.8266 (m-80) REVERT: I 326 MET cc_start: 0.6848 (tpt) cc_final: 0.6240 (tpt) REVERT: J 149 MET cc_start: 0.8937 (tpp) cc_final: 0.8497 (tpp) REVERT: J 150 VAL cc_start: 0.9404 (p) cc_final: 0.9183 (m) REVERT: J 265 ASP cc_start: 0.8933 (p0) cc_final: 0.8605 (p0) REVERT: J 282 PHE cc_start: 0.9089 (p90) cc_final: 0.8752 (p90) REVERT: J 357 ASP cc_start: 0.8692 (p0) cc_final: 0.8491 (p0) REVERT: J 364 GLU cc_start: 0.9226 (tt0) cc_final: 0.8971 (mm-30) REVERT: K 178 ASP cc_start: 0.9091 (p0) cc_final: 0.8769 (p0) REVERT: K 194 GLN cc_start: 0.8965 (mp10) cc_final: 0.8527 (mp10) REVERT: L 191 ARG cc_start: 0.9096 (mtp180) cc_final: 0.8058 (mmp80) REVERT: L 194 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7519 (ttp80) REVERT: L 263 ILE cc_start: 0.9252 (pt) cc_final: 0.9031 (pt) REVERT: L 266 MET cc_start: 0.9624 (ttp) cc_final: 0.9290 (ppp) REVERT: L 416 MET cc_start: 0.8993 (mmt) cc_final: 0.8771 (mmm) REVERT: M 188 LYS cc_start: 0.7094 (mttt) cc_final: 0.6260 (tppt) REVERT: M 203 ARG cc_start: 0.9290 (mmm160) cc_final: 0.9082 (tpp-160) REVERT: M 290 ARG cc_start: 0.5914 (pmt170) cc_final: 0.5432 (mtm180) REVERT: M 390 GLN cc_start: 0.8960 (mp10) cc_final: 0.8356 (mp10) REVERT: M 411 LYS cc_start: 0.8506 (ttmm) cc_final: 0.7912 (tptt) outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.3228 time to fit residues: 228.4348 Evaluate side-chains 330 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 275 optimal weight: 0.8980 chunk 289 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 GLN F 117 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 HIS J 240 HIS ** L 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24041 Z= 0.296 Angle : 0.692 9.208 32801 Z= 0.353 Chirality : 0.046 0.246 3934 Planarity : 0.004 0.060 4254 Dihedral : 8.054 102.544 3663 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.14), residues: 3262 helix: -1.26 (0.14), residues: 1212 sheet: -1.78 (0.22), residues: 470 loop : -2.05 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP M 376 HIS 0.013 0.001 HIS J 240 PHE 0.032 0.002 PHE A 218 TYR 0.023 0.002 TYR B 82 ARG 0.008 0.001 ARG I 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 2.734 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: A 218 PHE cc_start: 0.7842 (m-10) cc_final: 0.7609 (m-10) REVERT: A 221 ASN cc_start: 0.8475 (p0) cc_final: 0.8164 (p0) REVERT: A 229 THR cc_start: 0.8733 (m) cc_final: 0.8460 (p) REVERT: C 26 LEU cc_start: 0.8587 (pt) cc_final: 0.8360 (pt) REVERT: D 111 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.6911 (mtm-85) REVERT: F 137 TYR cc_start: 0.7794 (t80) cc_final: 0.7565 (t80) REVERT: G 38 ILE cc_start: 0.8896 (pt) cc_final: 0.8449 (mp) REVERT: H 249 TYR cc_start: 0.8470 (p90) cc_final: 0.8176 (p90) REVERT: H 310 GLU cc_start: 0.9093 (mp0) cc_final: 0.8700 (mp0) REVERT: H 356 ASN cc_start: 0.9522 (t0) cc_final: 0.9267 (t0) REVERT: I 208 TYR cc_start: 0.8555 (m-80) cc_final: 0.8226 (m-80) REVERT: I 255 LYS cc_start: 0.7640 (mmtm) cc_final: 0.6892 (mmtm) REVERT: I 281 ILE cc_start: 0.9264 (mm) cc_final: 0.8867 (mm) REVERT: I 326 MET cc_start: 0.6896 (tpt) cc_final: 0.6113 (tpt) REVERT: J 149 MET cc_start: 0.8952 (tpp) cc_final: 0.8508 (tpp) REVERT: J 150 VAL cc_start: 0.9406 (p) cc_final: 0.9192 (m) REVERT: J 265 ASP cc_start: 0.8906 (p0) cc_final: 0.8591 (p0) REVERT: J 282 PHE cc_start: 0.9107 (p90) cc_final: 0.8760 (p90) REVERT: J 357 ASP cc_start: 0.8681 (p0) cc_final: 0.8471 (p0) REVERT: J 364 GLU cc_start: 0.9207 (tt0) cc_final: 0.8977 (mm-30) REVERT: K 178 ASP cc_start: 0.9129 (p0) cc_final: 0.8839 (p0) REVERT: K 194 GLN cc_start: 0.8946 (mp10) cc_final: 0.8526 (mp10) REVERT: K 389 GLU cc_start: 0.8647 (tp30) cc_final: 0.8204 (tp30) REVERT: L 191 ARG cc_start: 0.9049 (mtp180) cc_final: 0.8809 (mtp180) REVERT: L 194 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7292 (ttp-110) REVERT: L 263 ILE cc_start: 0.9246 (pt) cc_final: 0.9036 (pt) REVERT: L 266 MET cc_start: 0.9628 (ttp) cc_final: 0.9282 (ppp) REVERT: L 279 PHE cc_start: 0.8835 (t80) cc_final: 0.8547 (t80) REVERT: L 282 GLU cc_start: 0.8151 (tp30) cc_final: 0.7481 (mm-30) REVERT: L 394 CYS cc_start: 0.9301 (t) cc_final: 0.9060 (t) REVERT: L 400 PHE cc_start: 0.7290 (m-10) cc_final: 0.7024 (m-10) REVERT: L 416 MET cc_start: 0.9028 (mmt) cc_final: 0.8583 (mmm) REVERT: M 188 LYS cc_start: 0.7080 (mttt) cc_final: 0.6258 (tppt) REVERT: M 203 ARG cc_start: 0.9292 (mmm160) cc_final: 0.9089 (tpp-160) REVERT: M 290 ARG cc_start: 0.5866 (pmt170) cc_final: 0.5227 (mtm180) REVERT: M 377 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8225 (tm-30) REVERT: M 390 GLN cc_start: 0.8977 (mp10) cc_final: 0.8354 (mp10) REVERT: M 411 LYS cc_start: 0.8538 (ttmm) cc_final: 0.7971 (tptt) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.3252 time to fit residues: 222.2220 Evaluate side-chains 334 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 213 optimal weight: 0.5980 chunk 322 optimal weight: 20.0000 chunk 297 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN D 117 GLN D 118 GLN F 5 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 GLN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 HIS ** L 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24041 Z= 0.238 Angle : 0.669 9.788 32801 Z= 0.334 Chirality : 0.045 0.238 3934 Planarity : 0.004 0.059 4254 Dihedral : 7.794 100.771 3663 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.05 % Allowed : 0.59 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.14), residues: 3262 helix: -1.07 (0.15), residues: 1208 sheet: -1.68 (0.22), residues: 472 loop : -1.94 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP M 376 HIS 0.007 0.001 HIS M 364 PHE 0.039 0.002 PHE H 343 TYR 0.022 0.002 TYR B 82 ARG 0.005 0.001 ARG I 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 432 time to evaluate : 2.752 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: A 221 ASN cc_start: 0.8502 (p0) cc_final: 0.8147 (p0) REVERT: A 229 THR cc_start: 0.8692 (m) cc_final: 0.8439 (p) REVERT: C 140 TYR cc_start: 0.6285 (t80) cc_final: 0.6040 (t80) REVERT: D 111 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.6857 (mtm-85) REVERT: E 78 MET cc_start: 0.8674 (pmm) cc_final: 0.8421 (pmm) REVERT: E 88 MET cc_start: 0.8521 (ptp) cc_final: 0.7933 (mtp) REVERT: F 137 TYR cc_start: 0.7849 (t80) cc_final: 0.7596 (t80) REVERT: G 33 ASN cc_start: 0.8822 (m-40) cc_final: 0.8503 (m110) REVERT: G 38 ILE cc_start: 0.8895 (pt) cc_final: 0.8450 (mp) REVERT: H 249 TYR cc_start: 0.8412 (p90) cc_final: 0.8081 (p90) REVERT: H 310 GLU cc_start: 0.9065 (mp0) cc_final: 0.8673 (mp0) REVERT: H 356 ASN cc_start: 0.9497 (t0) cc_final: 0.9249 (t0) REVERT: I 208 TYR cc_start: 0.8507 (m-80) cc_final: 0.8174 (m-80) REVERT: I 255 LYS cc_start: 0.7683 (mmtm) cc_final: 0.6870 (mmtm) REVERT: I 326 MET cc_start: 0.6920 (tpt) cc_final: 0.6222 (tpt) REVERT: J 149 MET cc_start: 0.8932 (tpp) cc_final: 0.8477 (tpp) REVERT: J 150 VAL cc_start: 0.9387 (p) cc_final: 0.9162 (m) REVERT: J 265 ASP cc_start: 0.8882 (p0) cc_final: 0.8640 (p0) REVERT: J 282 PHE cc_start: 0.9087 (p90) cc_final: 0.8736 (p90) REVERT: J 364 GLU cc_start: 0.9173 (tt0) cc_final: 0.8967 (mm-30) REVERT: K 178 ASP cc_start: 0.9108 (p0) cc_final: 0.8805 (p0) REVERT: K 194 GLN cc_start: 0.8923 (mp10) cc_final: 0.8549 (mp10) REVERT: K 389 GLU cc_start: 0.8671 (tp30) cc_final: 0.8173 (tp30) REVERT: L 191 ARG cc_start: 0.9070 (mtp180) cc_final: 0.8040 (mmp80) REVERT: L 194 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7796 (ttp80) REVERT: L 263 ILE cc_start: 0.9277 (pt) cc_final: 0.9067 (pt) REVERT: L 266 MET cc_start: 0.9605 (ttp) cc_final: 0.9300 (ppp) REVERT: L 279 PHE cc_start: 0.8891 (t80) cc_final: 0.8440 (t80) REVERT: L 282 GLU cc_start: 0.8051 (tp30) cc_final: 0.7431 (mm-30) REVERT: L 394 CYS cc_start: 0.9259 (t) cc_final: 0.8996 (t) REVERT: L 400 PHE cc_start: 0.7237 (m-10) cc_final: 0.6999 (m-10) REVERT: L 416 MET cc_start: 0.9032 (mmt) cc_final: 0.8529 (mmm) REVERT: M 188 LYS cc_start: 0.7058 (mttt) cc_final: 0.6247 (tppt) REVERT: M 290 ARG cc_start: 0.5767 (pmt170) cc_final: 0.5133 (mtm180) REVERT: M 390 GLN cc_start: 0.8944 (mp10) cc_final: 0.8409 (mp10) REVERT: M 411 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8022 (tptt) outliers start: 1 outliers final: 1 residues processed: 433 average time/residue: 0.3191 time to fit residues: 220.2009 Evaluate side-chains 341 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 118 GLN F 5 ASN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 HIS ** L 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.068438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.055803 restraints weight = 98425.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.057255 restraints weight = 63372.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.058268 restraints weight = 44665.509| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24041 Z= 0.180 Angle : 0.639 9.290 32801 Z= 0.317 Chirality : 0.044 0.216 3934 Planarity : 0.004 0.059 4254 Dihedral : 7.457 97.746 3663 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.15), residues: 3262 helix: -0.84 (0.15), residues: 1189 sheet: -1.51 (0.23), residues: 468 loop : -1.81 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 376 HIS 0.006 0.001 HIS G 73 PHE 0.015 0.001 PHE G 138 TYR 0.022 0.001 TYR B 82 ARG 0.006 0.001 ARG M 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4923.46 seconds wall clock time: 89 minutes 23.53 seconds (5363.53 seconds total)