Starting phenix.real_space_refine (version: dev) on Fri Feb 24 19:14:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/02_2023/6ef1_9043_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/02_2023/6ef1_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_9043/02_2023/6ef1_9043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/02_2023/6ef1_9043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/02_2023/6ef1_9043_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef1_9043/02_2023/6ef1_9043_updated.pdb" } resolution = 4.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 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-4877/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: 13.75, per 1000 atoms: 0.58 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: 10.32 Conformation dependent library (CDL) restraints added in 4.1 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: 1.98 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: 6.91 Time building geometry restraints manager: 10.90 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: 13994 26.49 - 52.98: 316 52.98 - 79.48: 35 79.48 - 105.97: 3 105.97 - 132.46: 1 Dihedral angle restraints: 14349 sinusoidal: 4880 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 14346 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 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. 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: 1.930 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: 10.420 Check model and map are aligned: 0.350 Process input model: 61.320 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 11.782 132.459 8261 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.47 % Favored : 85.50 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.4122 time to fit residues: 366.4543 Evaluate side-chains 349 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 3.059 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9749 ------------------------------------------------------------------------------- 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: 1.9990 chunk 245 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 165 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 139 HIS C 125 HIS ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 413 ASN I 312 GLN I 365 HIS I 418 GLN J 156 GLN J 331 HIS ** K 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 412 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.113 24041 Z= 0.347 Angle : 0.768 8.380 32801 Z= 0.402 Chirality : 0.047 0.280 3934 Planarity : 0.006 0.055 4254 Dihedral : 8.178 112.620 3539 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.45 % Favored : 89.52 % Rotamer Outliers : 0.18 % 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: -2.81 (0.12), residues: 1162 sheet: -3.37 (0.21), residues: 412 loop : -2.92 (0.15), residues: 1688 *********************** 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 486 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 482 time to evaluate : 3.327 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 outliers start: 4 outliers final: 0 residues processed: 485 average time/residue: 0.3652 time to fit residues: 275.5505 Evaluate side-chains 339 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6958 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 0.0670 chunk 244 optimal weight: 30.0000 chunk 200 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 chunk 318 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 292 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 236 optimal weight: 8.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- 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 A 209 HIS B 41 ASN D 230 ASN E 23 GLN E 91 HIS G 127 ASN H 392 HIS I 312 GLN J 204 HIS J 240 HIS K 182 GLN ** K 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 GLN ** L 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 24041 Z= 0.178 Angle : 0.654 8.491 32801 Z= 0.330 Chirality : 0.044 0.176 3934 Planarity : 0.004 0.054 4254 Dihedral : 7.135 107.693 3539 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.17 % Favored : 92.80 % Rotamer Outliers : 0.05 % 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: -3.55 (0.14), residues: 3262 helix: -2.01 (0.13), residues: 1189 sheet: -2.77 (0.22), residues: 446 loop : -2.45 (0.15), residues: 1627 *********************** 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 504 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 503 time to evaluate : 3.158 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 outliers start: 1 outliers final: 0 residues processed: 503 average time/residue: 0.3536 time to fit residues: 277.9613 Evaluate side-chains 360 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7678 ------------------------------------------------------------------------------- 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: 8.9990 chunk 221 optimal weight: 0.4980 chunk 152 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 313 optimal weight: 0.0770 chunk 154 optimal weight: 0.9990 chunk 280 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN J 204 HIS ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN ** 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: 0.7874 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 24041 Z= 0.170 Angle : 0.621 9.873 32801 Z= 0.312 Chirality : 0.044 0.241 3934 Planarity : 0.004 0.052 4254 Dihedral : 6.625 105.637 3539 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.11 % Favored : 92.86 % Rotamer Outliers : 0.00 % 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: -3.01 (0.14), residues: 3262 helix: -1.53 (0.14), residues: 1179 sheet: -2.23 (0.23), residues: 439 loop : -2.25 (0.15), residues: 1644 *********************** 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 476 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 2.696 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 outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 0.3420 time to fit residues: 258.2193 Evaluate side-chains 361 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4856 ------------------------------------------------------------------------------- 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: 40.0000 chunk 4 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 216 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN F 5 ASN G 23 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN I 426 ASN J 240 HIS L 273 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 24041 Z= 0.325 Angle : 0.697 9.243 32801 Z= 0.358 Chirality : 0.046 0.218 3934 Planarity : 0.004 0.054 4254 Dihedral : 6.769 105.320 3539 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer Outliers : 0.00 % 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: -2.89 (0.14), residues: 3262 helix: -1.41 (0.14), residues: 1200 sheet: -2.09 (0.23), residues: 441 loop : -2.24 (0.15), residues: 1621 *********************** 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 434 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.3529 time to fit residues: 240.8093 Evaluate side-chains 338 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8004 ------------------------------------------------------------------------------- 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: 9.9990 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 260 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN D 117 GLN ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN G 204 HIS ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN J 240 HIS K 194 GLN K 264 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 24041 Z= 0.277 Angle : 0.672 10.273 32801 Z= 0.342 Chirality : 0.045 0.262 3934 Planarity : 0.004 0.075 4254 Dihedral : 6.624 102.438 3539 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.05 % 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: -2.74 (0.14), residues: 3262 helix: -1.33 (0.14), residues: 1203 sheet: -1.87 (0.23), residues: 452 loop : -2.15 (0.15), residues: 1607 *********************** 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 431 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 430 time to evaluate : 2.842 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 outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.3618 time to fit residues: 248.7480 Evaluate side-chains 351 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6587 ------------------------------------------------------------------------------- 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: 6.9990 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 312 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 209 HIS B 41 ASN D 117 GLN ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 204 HIS I 204 HIS ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 24041 Z= 0.306 Angle : 0.687 9.806 32801 Z= 0.351 Chirality : 0.046 0.186 3934 Planarity : 0.004 0.055 4254 Dihedral : 6.666 102.325 3539 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer Outliers : 0.00 % 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: -2.66 (0.14), residues: 3262 helix: -1.26 (0.14), residues: 1196 sheet: -1.75 (0.23), residues: 449 loop : -2.14 (0.15), residues: 1617 *********************** 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 439 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 2.907 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 outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.3354 time to fit residues: 234.9600 Evaluate side-chains 344 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5858 ------------------------------------------------------------------------------- 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: 0.5980 chunk 124 optimal weight: 0.0970 chunk 186 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 overall best weight: 2.7382 ------------------------------------------------------------------------------- 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 ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN G 170 GLN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN ** 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: 0.7977 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 24041 Z= 0.226 Angle : 0.652 8.985 32801 Z= 0.329 Chirality : 0.044 0.182 3934 Planarity : 0.004 0.055 4254 Dihedral : 6.373 100.255 3539 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 0.05 % 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: -1.08 (0.15), residues: 1195 sheet: -1.55 (0.23), residues: 454 loop : -1.99 (0.15), residues: 1613 *********************** 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 450 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.3319 time to fit residues: 239.3780 Evaluate side-chains 337 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0725 ------------------------------------------------------------------------------- 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: 10.0000 chunk 299 optimal weight: 4.9990 chunk 272 optimal weight: 0.0470 chunk 291 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN F 117 GLN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN ** 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: 0.7943 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 24041 Z= 0.176 Angle : 0.638 10.156 32801 Z= 0.316 Chirality : 0.044 0.167 3934 Planarity : 0.004 0.070 4254 Dihedral : 6.089 97.613 3539 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer Outliers : 0.00 % 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: -2.20 (0.15), residues: 3262 helix: -0.91 (0.15), residues: 1194 sheet: -1.43 (0.23), residues: 463 loop : -1.86 (0.16), residues: 1605 *********************** 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 462 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.3447 time to fit residues: 256.5544 Evaluate side-chains 348 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.851 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5769 ------------------------------------------------------------------------------- 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: 8.9990 chunk 307 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 GLN E 99 HIS F 5 ASN G 23 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 24041 Z= 0.480 Angle : 0.840 11.640 32801 Z= 0.433 Chirality : 0.050 0.289 3934 Planarity : 0.005 0.053 4254 Dihedral : 6.858 101.511 3539 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer Outliers : 0.00 % 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: -2.76 (0.14), residues: 3262 helix: -1.36 (0.14), residues: 1223 sheet: -1.84 (0.22), residues: 470 loop : -2.17 (0.15), residues: 1569 ********************** 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 408 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3303 time to fit residues: 216.6393 Evaluate side-chains 314 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6896 ------------------------------------------------------------------------------- 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: 6.9990 chunk 273 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** B 149 GLN C 124 GLN D 117 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 117 GLN G 127 ASN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.068193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.055568 restraints weight = 98496.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.057000 restraints weight = 64329.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.058012 restraints weight = 45578.717| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 24041 Z= 0.209 Angle : 0.668 9.948 32801 Z= 0.333 Chirality : 0.045 0.249 3934 Planarity : 0.004 0.054 4254 Dihedral : 6.288 98.463 3539 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 0.05 % 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: -2.39 (0.14), residues: 3262 helix: -1.08 (0.15), residues: 1212 sheet: -1.62 (0.23), residues: 460 loop : -1.92 (0.16), residues: 1590 =============================================================================== Job complete usr+sys time: 4895.18 seconds wall clock time: 90 minutes 4.53 seconds (5404.53 seconds total)