Starting phenix.real_space_refine on Fri Mar 6 20:16:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmj_22259/03_2026/6xmj_22259.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmj_22259/03_2026/6xmj_22259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xmj_22259/03_2026/6xmj_22259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmj_22259/03_2026/6xmj_22259.map" model { file = "/net/cci-nas-00/data/ceres_data/6xmj_22259/03_2026/6xmj_22259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmj_22259/03_2026/6xmj_22259.cif" } resolution = 3.0 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 182 5.16 5 C 22036 2.51 5 N 6025 2.21 5 O 6674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34917 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1810 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1666 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 216} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1854 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 238} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1724 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 6, 'TRANS': 235} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 11, 'PHE:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1707 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1854 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1509 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1637 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 209} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1615 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Chain: "Q" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1579 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Chain: "S" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Chain: "T" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Chain: "U" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Time building chain proxies: 7.27, per 1000 atoms: 0.21 Number of scatterers: 34917 At special positions: 0 Unit cell: (134.93, 182.31, 144.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 182 16.00 O 6674 8.00 N 6025 7.00 C 22036 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 - 3.00 Amino acid : True - 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: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8458 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 38 sheets defined 52.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.624A pdb=" N ARG A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.809A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 removed outlier: 4.001A pdb=" N PHE A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.435A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 242 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.543A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 101 removed outlier: 3.726A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.657A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.672A pdb=" N LEU B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.619A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.544A pdb=" N ASN C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.569A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.565A pdb=" N ALA C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 removed outlier: 3.501A pdb=" N LYS C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 229 through 250 removed outlier: 3.761A pdb=" N GLN C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.684A pdb=" N ALA D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 25 " --> pdb=" O TYR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 59 removed outlier: 3.535A pdb=" N VAL D 59 " --> pdb=" O GLU D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 59' Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.650A pdb=" N ALA D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 92 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 Processing helix chain 'D' and resid 164 through 176 removed outlier: 4.248A pdb=" N GLU D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.769A pdb=" N VAL D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 240 removed outlier: 3.805A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 82 through 104 Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 4.757A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 removed outlier: 3.629A pdb=" N GLN E 204 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 239 removed outlier: 3.676A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.526A pdb=" N GLU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.698A pdb=" N LEU F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.477A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG F 174 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 removed outlier: 3.720A pdb=" N PHE F 179 " --> pdb=" O HIS F 175 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET F 180 " --> pdb=" O MET F 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 175 through 180' Processing helix chain 'F' and resid 183 through 197 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 20 through 32 removed outlier: 3.724A pdb=" N GLU G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 122 through 124 No H-bonds generated for 'chain 'G' and resid 122 through 124' Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.531A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 184 Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.236A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 228 through 242 removed outlier: 3.646A pdb=" N TYR G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.737A pdb=" N ALA H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 134 Processing helix chain 'H' and resid 135 through 143 removed outlier: 3.625A pdb=" N ASP H 140 " --> pdb=" O TYR H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 167 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'I' and resid 48 through 71 removed outlier: 3.814A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.752A pdb=" N ALA I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.752A pdb=" N ASP I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 Processing helix chain 'J' and resid 3 through 7 removed outlier: 3.772A pdb=" N ASN J 7 " --> pdb=" O MET J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 78 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.779A pdb=" N SER J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 removed outlier: 3.810A pdb=" N GLU J 165 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET J 171 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN J 173 " --> pdb=" O GLN J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 72 removed outlier: 3.787A pdb=" N THR K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS K 68 " --> pdb=" O VAL K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 91 removed outlier: 3.566A pdb=" N ASN K 82 " --> pdb=" O THR K 78 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS K 91 " --> pdb=" O ASN K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 5.027A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU K 143 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 48 through 71 removed outlier: 3.516A pdb=" N ILE L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 removed outlier: 3.526A pdb=" N LEU L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 131 through 142 removed outlier: 3.940A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.695A pdb=" N ARG L 166 " --> pdb=" O GLN L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 201 removed outlier: 3.785A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.589A pdb=" N THR M 65 " --> pdb=" O CYS M 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET M 74 " --> pdb=" O ALA M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'M' and resid 141 through 153 removed outlier: 3.567A pdb=" N GLN M 146 " --> pdb=" O SER M 142 " (cutoff:3.500A) Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 183 Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.865A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 101 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 3.632A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'N' and resid 209 through 214 removed outlier: 3.704A pdb=" N ALA N 212 " --> pdb=" O TRP N 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 14 Processing helix chain 'O' and resid 17 through 31 removed outlier: 3.604A pdb=" N SER O 21 " --> pdb=" O THR O 17 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL O 24 " --> pdb=" O SER O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 52 Processing helix chain 'O' and resid 56 through 62 removed outlier: 3.556A pdb=" N GLN O 59 " --> pdb=" O GLY O 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS O 62 " --> pdb=" O GLN O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 94 removed outlier: 4.013A pdb=" N LEU O 68 " --> pdb=" O PRO O 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL O 70 " --> pdb=" O GLN O 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR O 87 " --> pdb=" O CYS O 83 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE O 88 " --> pdb=" O GLN O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 125 removed outlier: 3.771A pdb=" N VAL O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE O 122 " --> pdb=" O ASP O 118 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS O 123 " --> pdb=" O GLU O 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU O 125 " --> pdb=" O GLU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 161 removed outlier: 3.950A pdb=" N GLU O 147 " --> pdb=" O TYR O 143 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA O 151 " --> pdb=" O GLU O 147 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS O 158 " --> pdb=" O THR O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 214 removed outlier: 3.769A pdb=" N LEU O 180 " --> pdb=" O SER O 176 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG O 184 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE O 190 " --> pdb=" O ILE O 186 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET O 191 " --> pdb=" O ASP O 187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR O 199 " --> pdb=" O GLU O 195 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 215 through 221 removed outlier: 3.515A pdb=" N ILE O 220 " --> pdb=" O TRP O 216 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 16 removed outlier: 3.673A pdb=" N SER P 15 " --> pdb=" O ASN P 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 31 removed outlier: 3.804A pdb=" N VAL P 24 " --> pdb=" O SER P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 52 Processing helix chain 'P' and resid 56 through 61 removed outlier: 3.541A pdb=" N GLU P 61 " --> pdb=" O ALA P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 94 removed outlier: 3.546A pdb=" N LEU P 68 " --> pdb=" O PRO P 64 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL P 70 " --> pdb=" O GLN P 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN P 84 " --> pdb=" O ASN P 80 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR P 87 " --> pdb=" O CYS P 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE P 88 " --> pdb=" O GLN P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 123 removed outlier: 3.531A pdb=" N ILE P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 161 removed outlier: 3.690A pdb=" N GLU P 147 " --> pdb=" O TYR P 143 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA P 151 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS P 158 " --> pdb=" O THR P 154 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 214 removed outlier: 3.807A pdb=" N LEU P 180 " --> pdb=" O SER P 176 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG P 184 " --> pdb=" O LEU P 180 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET P 191 " --> pdb=" O ASP P 187 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR P 199 " --> pdb=" O GLU P 195 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR P 203 " --> pdb=" O THR P 199 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL P 208 " --> pdb=" O MET P 204 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 14 Processing helix chain 'Q' and resid 17 through 31 removed outlier: 3.629A pdb=" N SER Q 21 " --> pdb=" O THR Q 17 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL Q 24 " --> pdb=" O SER Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 52 removed outlier: 3.564A pdb=" N ASN Q 52 " --> pdb=" O GLY Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 62 Processing helix chain 'Q' and resid 64 through 94 removed outlier: 3.553A pdb=" N LEU Q 68 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL Q 70 " --> pdb=" O GLN Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 126 removed outlier: 3.796A pdb=" N VAL Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS Q 123 " --> pdb=" O GLU Q 119 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR Q 124 " --> pdb=" O LEU Q 120 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY Q 126 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 161 removed outlier: 3.630A pdb=" N GLU Q 147 " --> pdb=" O TYR Q 143 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL Q 155 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 221 removed outlier: 4.374A pdb=" N LEU Q 180 " --> pdb=" O SER Q 176 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU Q 181 " --> pdb=" O PRO Q 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA Q 188 " --> pdb=" O ARG Q 184 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET Q 191 " --> pdb=" O ASP Q 187 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR Q 203 " --> pdb=" O THR Q 199 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS Q 217 " --> pdb=" O LEU Q 213 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS Q 218 " --> pdb=" O LEU Q 214 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE Q 220 " --> pdb=" O TRP Q 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN Q 221 " --> pdb=" O LYS Q 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 16 removed outlier: 3.589A pdb=" N SER R 15 " --> pdb=" O ASN R 11 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR R 16 " --> pdb=" O LEU R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 52 removed outlier: 3.719A pdb=" N SER R 21 " --> pdb=" O THR R 17 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 24 " --> pdb=" O SER R 20 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR R 32 " --> pdb=" O TRP R 28 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 60 Processing helix chain 'R' and resid 64 through 94 removed outlier: 3.734A pdb=" N LEU R 68 " --> pdb=" O PRO R 64 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL R 70 " --> pdb=" O GLN R 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN R 80 " --> pdb=" O ASP R 76 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR R 87 " --> pdb=" O CYS R 83 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE R 88 " --> pdb=" O GLN R 84 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 122 removed outlier: 3.586A pdb=" N ILE R 117 " --> pdb=" O VAL R 113 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 157 removed outlier: 3.624A pdb=" N GLU R 147 " --> pdb=" O TYR R 143 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU R 149 " --> pdb=" O LEU R 145 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 214 removed outlier: 3.888A pdb=" N LEU R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE R 190 " --> pdb=" O ILE R 186 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR R 203 " --> pdb=" O THR R 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 221 Processing helix chain 'R' and resid 227 through 231 Processing helix chain 'S' and resid 5 through 16 removed outlier: 3.540A pdb=" N SER S 15 " --> pdb=" O ASN S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 31 removed outlier: 3.581A pdb=" N VAL S 24 " --> pdb=" O SER S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 52 removed outlier: 3.739A pdb=" N VAL S 49 " --> pdb=" O GLU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 62 removed outlier: 3.733A pdb=" N LYS S 62 " --> pdb=" O GLN S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 94 removed outlier: 3.792A pdb=" N LEU S 68 " --> pdb=" O PRO S 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL S 70 " --> pdb=" O GLN S 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE S 88 " --> pdb=" O GLN S 84 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 94 " --> pdb=" O THR S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 126 removed outlier: 4.008A pdb=" N THR S 124 " --> pdb=" O LEU S 120 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY S 126 " --> pdb=" O ILE S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 161 removed outlier: 3.970A pdb=" N VAL S 155 " --> pdb=" O ALA S 151 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP S 157 " --> pdb=" O SER S 153 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU S 160 " --> pdb=" O GLU S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 221 removed outlier: 3.801A pdb=" N LEU S 180 " --> pdb=" O SER S 176 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE S 190 " --> pdb=" O ILE S 186 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET S 191 " --> pdb=" O ASP S 187 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR S 199 " --> pdb=" O GLU S 195 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR S 203 " --> pdb=" O THR S 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN S 210 " --> pdb=" O ARG S 206 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS S 217 " --> pdb=" O LEU S 213 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS S 218 " --> pdb=" O LEU S 214 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE S 220 " --> pdb=" O TRP S 216 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN S 221 " --> pdb=" O LYS S 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 14 Processing helix chain 'T' and resid 17 through 31 removed outlier: 3.579A pdb=" N VAL T 24 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 52 removed outlier: 3.552A pdb=" N ASN T 52 " --> pdb=" O GLY T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 61 removed outlier: 3.538A pdb=" N GLN T 59 " --> pdb=" O GLY T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 94 removed outlier: 3.922A pdb=" N LEU T 68 " --> pdb=" O PRO T 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE T 88 " --> pdb=" O GLN T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 Processing helix chain 'T' and resid 143 through 160 removed outlier: 3.668A pdb=" N LEU T 149 " --> pdb=" O LEU T 145 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS T 158 " --> pdb=" O THR T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 221 removed outlier: 3.898A pdb=" N LEU T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET T 191 " --> pdb=" O ASP T 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET T 204 " --> pdb=" O HIS T 200 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA T 207 " --> pdb=" O THR T 203 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN T 210 " --> pdb=" O ARG T 206 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS T 217 " --> pdb=" O LEU T 213 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS T 218 " --> pdb=" O LEU T 214 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN T 221 " --> pdb=" O LYS T 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 16 removed outlier: 3.733A pdb=" N ILE U 9 " --> pdb=" O ARG U 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER U 15 " --> pdb=" O ASN U 11 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR U 16 " --> pdb=" O LEU U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 31 removed outlier: 3.660A pdb=" N SER U 21 " --> pdb=" O THR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 52 removed outlier: 4.358A pdb=" N GLU U 37 " --> pdb=" O LEU U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 Processing helix chain 'U' and resid 64 through 94 removed outlier: 3.847A pdb=" N LEU U 68 " --> pdb=" O PRO U 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY U 69 " --> pdb=" O GLU U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 120 removed outlier: 3.543A pdb=" N ALA U 108 " --> pdb=" O ASN U 104 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL U 109 " --> pdb=" O LEU U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 144 through 161 removed outlier: 3.676A pdb=" N VAL U 155 " --> pdb=" O ALA U 151 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS U 158 " --> pdb=" O THR U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 221 removed outlier: 3.732A pdb=" N LEU U 180 " --> pdb=" O SER U 176 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG U 184 " --> pdb=" O LEU U 180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE U 190 " --> pdb=" O ILE U 186 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET U 191 " --> pdb=" O ASP U 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR U 199 " --> pdb=" O GLU U 195 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS U 217 " --> pdb=" O LEU U 213 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS U 218 " --> pdb=" O LEU U 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.256A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 53 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.586A pdb=" N MET A 138 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY A 162 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 69 removed outlier: 6.524A pdb=" N MET C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 134 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 138 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY C 158 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 removed outlier: 3.562A pdb=" N GLU E 216 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.389A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 163 " --> pdb=" O HIS E 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.389A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 removed outlier: 5.197A pdb=" N GLY F 216 " --> pdb=" O GLU F 220 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.479A pdb=" N ILE F 70 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.501A pdb=" N VAL G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.524A pdb=" N GLN H 187 " --> pdb=" O LEU H 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.875A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR H 25 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 36 removed outlier: 3.602A pdb=" N VAL H 121 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 124 through 128 removed outlier: 7.422A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS I 182 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 removed outlier: 6.870A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.139A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 211 through 218 removed outlier: 6.608A pdb=" N THR J 199 " --> pdb=" O LEU I 212 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU I 214 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR J 197 " --> pdb=" O GLU I 214 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE I 216 " --> pdb=" O ILE J 195 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE J 195 " --> pdb=" O ILE I 216 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 20 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.471A pdb=" N ILE J 30 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N MET J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 44 Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC8, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC9, first strand: chain 'K' and resid 21 through 22 removed outlier: 6.686A pdb=" N ALA K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 35 through 37 removed outlier: 3.510A pdb=" N LEU K 102 " --> pdb=" O MET K 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 125 through 129 removed outlier: 5.810A pdb=" N VAL L 174 " --> pdb=" O SER L 189 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER L 189 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU L 176 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY L 183 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.780A pdb=" N SER L 28 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.570A pdb=" N ILE L 37 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.709A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.709A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.853A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 43 through 45 removed outlier: 3.698A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.693A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.693A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR N 132 " --> pdb=" O TYR N 124 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 136 through 138 2124 hydrogen bonds defined for protein. 6108 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: 6.92 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7388 1.33 - 1.45: 7804 1.45 - 1.57: 20007 1.57 - 1.69: 0 1.69 - 1.81: 295 Bond restraints: 35494 Sorted by residual: bond pdb=" N ARG E 10 " pdb=" CA ARG E 10 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.21e-02 6.83e+03 8.93e+00 bond pdb=" N ARG C 17 " pdb=" CA ARG C 17 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.29e-02 6.01e+03 8.17e+00 bond pdb=" N LEU T 227 " pdb=" CA LEU T 227 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.46e+00 bond pdb=" N ASP E 9 " pdb=" CA ASP E 9 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.14e+00 bond pdb=" N ALA J 32 " pdb=" CA ALA J 32 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.19e-02 7.06e+03 6.03e+00 ... (remaining 35489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 45395 1.44 - 2.89: 2253 2.89 - 4.33: 312 4.33 - 5.77: 95 5.77 - 7.21: 10 Bond angle restraints: 48065 Sorted by residual: angle pdb=" N ILE B 67 " pdb=" CA ILE B 67 " pdb=" C ILE B 67 " ideal model delta sigma weight residual 111.81 108.11 3.70 8.60e-01 1.35e+00 1.85e+01 angle pdb=" CA ASP E 9 " pdb=" C ASP E 9 " pdb=" O ASP E 9 " ideal model delta sigma weight residual 120.55 116.03 4.52 1.06e+00 8.90e-01 1.81e+01 angle pdb=" CA PHE J 28 " pdb=" C PHE J 28 " pdb=" O PHE J 28 " ideal model delta sigma weight residual 120.36 115.87 4.49 1.08e+00 8.57e-01 1.73e+01 angle pdb=" N SER I 171 " pdb=" CA SER I 171 " pdb=" CB SER I 171 " ideal model delta sigma weight residual 114.17 109.57 4.60 1.14e+00 7.69e-01 1.63e+01 angle pdb=" N GLY C 125 " pdb=" CA GLY C 125 " pdb=" C GLY C 125 " ideal model delta sigma weight residual 111.34 118.55 -7.21 1.82e+00 3.02e-01 1.57e+01 ... (remaining 48060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19667 17.96 - 35.92: 1432 35.92 - 53.88: 213 53.88 - 71.84: 55 71.84 - 89.80: 23 Dihedral angle restraints: 21390 sinusoidal: 8206 harmonic: 13184 Sorted by residual: dihedral pdb=" CA GLY M 190 " pdb=" C GLY M 190 " pdb=" N ASP M 191 " pdb=" CA ASP M 191 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLU P 121 " pdb=" C GLU P 121 " pdb=" N ILE P 122 " pdb=" CA ILE P 122 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU B 73 " pdb=" C LEU B 73 " pdb=" N VAL B 74 " pdb=" CA VAL B 74 " ideal model delta harmonic sigma weight residual 180.00 155.88 24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 21387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3801 0.040 - 0.080: 1297 0.080 - 0.120: 346 0.120 - 0.160: 84 0.160 - 0.200: 5 Chirality restraints: 5533 Sorted by residual: chirality pdb=" CA ILE J 30 " pdb=" N ILE J 30 " pdb=" C ILE J 30 " pdb=" CB ILE J 30 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE J 30 " pdb=" CA ILE J 30 " pdb=" CG1 ILE J 30 " pdb=" CG2 ILE J 30 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA LEU C 18 " pdb=" N LEU C 18 " pdb=" C LEU C 18 " pdb=" CB LEU C 18 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 5530 not shown) Planarity restraints: 6190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 16 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C GLY C 16 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY C 16 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 17 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN N 147 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO N 148 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO N 148 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 148 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER O 63 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO O 64 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO O 64 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 64 " -0.031 5.00e-02 4.00e+02 ... (remaining 6187 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2408 2.74 - 3.28: 34282 3.28 - 3.82: 54807 3.82 - 4.36: 70466 4.36 - 4.90: 122195 Nonbonded interactions: 284158 Sorted by model distance: nonbonded pdb=" O ALA P 30 " pdb=" NE2 GLN P 34 " model vdw 2.202 3.120 nonbonded pdb=" NH1 ARG Q 152 " pdb=" OE2 GLU Q 156 " model vdw 2.209 3.120 nonbonded pdb=" NH1 ARG P 152 " pdb=" OE2 GLU P 156 " model vdw 2.213 3.120 nonbonded pdb=" NH1 ARG L 61 " pdb=" OE1 GLN L 62 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG I 203 " pdb=" OE1 GLU J 155 " model vdw 2.221 3.120 ... (remaining 284153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'O' and (resid 4 through 226 or (resid 227 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = chain 'Q' selection = (chain 'R' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'S' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'T' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.080 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.160 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.005 0.052 35494 Z= 0.210 Angle : 0.739 7.214 48065 Z= 0.418 Chirality : 0.044 0.200 5533 Planarity : 0.005 0.056 6190 Dihedral : 13.220 89.797 12932 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 0.03 % Allowed : 0.85 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.11), residues: 4483 helix: -1.32 (0.10), residues: 2198 sheet: -1.55 (0.17), residues: 745 loop : -2.21 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 132 TYR 0.025 0.002 TYR M 130 PHE 0.028 0.002 PHE L 8 TRP 0.015 0.001 TRP P 216 HIS 0.013 0.001 HIS O 47 Details of bonding type rmsd covalent geometry : bond 0.00458 (35494) covalent geometry : angle 0.73886 (48065) hydrogen bonds : bond 0.19315 ( 2086) hydrogen bonds : angle 6.94507 ( 6108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 920 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7651 (ttmt) REVERT: C 69 ASN cc_start: 0.7365 (t0) cc_final: 0.6937 (t0) REVERT: C 75 SER cc_start: 0.9208 (t) cc_final: 0.8910 (t) REVERT: D 213 ARG cc_start: 0.4970 (mmp-170) cc_final: 0.3984 (mtm180) REVERT: F 170 THR cc_start: 0.9170 (m) cc_final: 0.8963 (m) REVERT: I 195 LYS cc_start: 0.5885 (mmtt) cc_final: 0.5097 (tttp) REVERT: L 105 ASP cc_start: 0.7861 (p0) cc_final: 0.7658 (p0) REVERT: L 167 ASP cc_start: 0.7850 (t0) cc_final: 0.7650 (t0) REVERT: M 26 ASP cc_start: 0.7699 (p0) cc_final: 0.7370 (p0) REVERT: R 100 LYS cc_start: 0.8557 (mttm) cc_final: 0.8335 (mtmt) outliers start: 1 outliers final: 0 residues processed: 921 average time/residue: 0.8228 time to fit residues: 874.4727 Evaluate side-chains 590 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 95 GLN B 111 GLN C 123 GLN C 155 ASN E 41 GLN E 104 ASN E 152 GLN E 204 GLN E 225 ASN F 60 GLN F 146 GLN F 166 GLN G 68 ASN H 38 HIS H 62 GLN H 106 GLN I 153 ASN I 172 ASN K 61 GLN K 63 ASN K 71 ASN K 87 ASN L 29 GLN L 38 ASN L 85 ASN N 157 GLN O 66 GLN O 221 GLN P 11 ASN P 84 GLN Q 11 ASN Q 34 GLN Q 111 HIS R 84 GLN R 221 GLN S 10 GLN S 34 GLN S 66 GLN S 72 GLN S 221 GLN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS T 185 GLN T 221 GLN U 66 GLN U 72 GLN U 80 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111365 restraints weight = 42433.351| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.05 r_work: 0.2993 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35494 Z= 0.134 Angle : 0.540 7.420 48065 Z= 0.294 Chirality : 0.042 0.175 5533 Planarity : 0.004 0.055 6190 Dihedral : 4.839 83.131 4979 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.26 % Allowed : 12.34 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.12), residues: 4483 helix: 0.56 (0.11), residues: 2210 sheet: -0.74 (0.17), residues: 766 loop : -1.56 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 57 TYR 0.017 0.001 TYR K 117 PHE 0.016 0.001 PHE P 190 TRP 0.009 0.001 TRP E 100 HIS 0.007 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00294 (35494) covalent geometry : angle 0.53961 (48065) hydrogen bonds : bond 0.04588 ( 2086) hydrogen bonds : angle 4.42804 ( 6108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 671 time to evaluate : 1.375 Fit side-chains REVERT: A 203 SER cc_start: 0.8910 (m) cc_final: 0.8642 (p) REVERT: B 227 ASP cc_start: 0.7611 (m-30) cc_final: 0.7323 (m-30) REVERT: C 69 ASN cc_start: 0.7837 (t0) cc_final: 0.7387 (t0) REVERT: C 246 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6667 (mmmm) REVERT: D 38 ARG cc_start: 0.6761 (mpp80) cc_final: 0.6483 (mpp80) REVERT: D 61 LYS cc_start: 0.8285 (tppp) cc_final: 0.7777 (tptm) REVERT: D 213 ARG cc_start: 0.5300 (mmp-170) cc_final: 0.3292 (mtm180) REVERT: G 150 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8150 (ttm) REVERT: G 232 ARG cc_start: 0.8300 (mtm110) cc_final: 0.8059 (ttm-80) REVERT: G 238 TYR cc_start: 0.8577 (t80) cc_final: 0.8325 (t80) REVERT: H 71 ASN cc_start: 0.8654 (t0) cc_final: 0.8434 (t0) REVERT: H 92 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: I 89 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8142 (ttm110) REVERT: I 195 LYS cc_start: 0.6176 (mmtt) cc_final: 0.4403 (tttt) REVERT: I 216 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8195 (mm) REVERT: J 159 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7508 (p0) REVERT: K 27 GLN cc_start: 0.8364 (mt0) cc_final: 0.7382 (pp30) REVERT: K 168 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8764 (mp10) REVERT: M 39 ASP cc_start: 0.7957 (t0) cc_final: 0.7652 (t0) REVERT: N 186 ARG cc_start: 0.8535 (mtp180) cc_final: 0.8207 (mtm180) REVERT: O 41 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7900 (ttpt) REVERT: O 89 ARG cc_start: 0.8882 (ttm-80) cc_final: 0.8585 (ttm170) REVERT: O 204 MET cc_start: 0.8662 (mmp) cc_final: 0.8451 (mmm) REVERT: P 147 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: R 100 LYS cc_start: 0.8845 (mttm) cc_final: 0.8462 (mtmt) REVERT: S 89 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8157 (ttm-80) REVERT: T 55 TYR cc_start: 0.8867 (m-10) cc_final: 0.8626 (m-80) REVERT: T 65 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: U 50 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8526 (mm) outliers start: 82 outliers final: 17 residues processed: 715 average time/residue: 0.7455 time to fit residues: 623.3781 Evaluate side-chains 606 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 580 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 168 GLN Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 312 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 382 optimal weight: 9.9990 chunk 386 optimal weight: 10.0000 chunk 368 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 166 ASN D 92 GLN D 146 GLN D 175 ASN E 225 ASN F 5 GLN F 60 GLN G 68 ASN G 101 ASN H 106 GLN I 57 GLN I 153 ASN J 40 GLN K 101 ASN L 38 ASN N 89 HIS O 210 ASN P 11 ASN Q 11 ASN Q 72 GLN Q 210 ASN S 75 GLN S 210 ASN S 221 GLN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN U 11 ASN U 72 GLN U 210 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.114591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.096202 restraints weight = 44291.932| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.14 r_work: 0.2819 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 35494 Z= 0.285 Angle : 0.679 11.718 48065 Z= 0.359 Chirality : 0.048 0.175 5533 Planarity : 0.005 0.055 6190 Dihedral : 5.243 87.651 4979 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.28 % Allowed : 14.58 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.12), residues: 4483 helix: 0.78 (0.11), residues: 2215 sheet: -0.18 (0.18), residues: 780 loop : -1.46 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 226 TYR 0.021 0.002 TYR P 229 PHE 0.020 0.002 PHE J 69 TRP 0.018 0.002 TRP H 103 HIS 0.006 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00694 (35494) covalent geometry : angle 0.67924 (48065) hydrogen bonds : bond 0.06123 ( 2086) hydrogen bonds : angle 4.54616 ( 6108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 588 time to evaluate : 1.223 Fit side-chains REVERT: A 100 ASN cc_start: 0.8810 (t0) cc_final: 0.8533 (t0) REVERT: B 49 LYS cc_start: 0.8375 (tttt) cc_final: 0.7894 (ttpp) REVERT: B 227 ASP cc_start: 0.7715 (m-30) cc_final: 0.7440 (m-30) REVERT: C 141 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8850 (pttt) REVERT: C 219 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: C 246 LYS cc_start: 0.7318 (mtpt) cc_final: 0.6832 (mmmm) REVERT: D 61 LYS cc_start: 0.8435 (tppp) cc_final: 0.8038 (tptm) REVERT: D 211 MET cc_start: 0.8953 (ttp) cc_final: 0.8706 (ttt) REVERT: D 213 ARG cc_start: 0.5870 (mmp-170) cc_final: 0.3685 (mtm180) REVERT: E 122 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.6206 (mm110) REVERT: E 228 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8478 (ttm) REVERT: E 239 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7875 (ptmt) REVERT: F 16 GLN cc_start: 0.8738 (mp-120) cc_final: 0.8511 (mp10) REVERT: F 86 ASN cc_start: 0.8848 (m110) cc_final: 0.8574 (m-40) REVERT: F 185 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7596 (m110) REVERT: G 238 TYR cc_start: 0.8557 (t80) cc_final: 0.8323 (t80) REVERT: H 92 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: H 196 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8250 (mmtt) REVERT: I 143 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8455 (mtp180) REVERT: I 195 LYS cc_start: 0.6356 (mmtt) cc_final: 0.4489 (tttt) REVERT: I 216 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8712 (mm) REVERT: J 159 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7965 (p0) REVERT: K 2 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: K 27 GLN cc_start: 0.8458 (mt0) cc_final: 0.7617 (pp30) REVERT: K 154 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: L 141 ARG cc_start: 0.8473 (mmp-170) cc_final: 0.7350 (mtt180) REVERT: M 105 TYR cc_start: 0.8967 (t80) cc_final: 0.8725 (t80) REVERT: M 144 MET cc_start: 0.9104 (mtt) cc_final: 0.8832 (mtm) REVERT: N 73 ASP cc_start: 0.8338 (m-30) cc_final: 0.7877 (m-30) REVERT: N 186 ARG cc_start: 0.8674 (mtp180) cc_final: 0.8380 (mtm180) REVERT: O 10 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8060 (tp40) REVERT: O 76 ASP cc_start: 0.8468 (m-30) cc_final: 0.8101 (m-30) REVERT: O 80 ASN cc_start: 0.9099 (m-40) cc_final: 0.8870 (m-40) REVERT: P 147 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8163 (tp30) REVERT: Q 76 ASP cc_start: 0.8559 (m-30) cc_final: 0.8230 (m-30) REVERT: R 100 LYS cc_start: 0.8910 (mttm) cc_final: 0.8557 (mtmt) REVERT: R 226 ASN cc_start: 0.6973 (t0) cc_final: 0.6611 (t0) REVERT: S 89 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8506 (ttm-80) REVERT: S 157 ASP cc_start: 0.8473 (t70) cc_final: 0.8259 (t70) REVERT: T 41 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8131 (mmmm) REVERT: T 55 TYR cc_start: 0.8885 (m-10) cc_final: 0.8633 (m-80) REVERT: T 119 GLU cc_start: 0.8058 (tp30) cc_final: 0.7589 (mt-10) REVERT: U 10 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8580 (mm110) REVERT: U 115 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8664 (mtmt) outliers start: 119 outliers final: 49 residues processed: 655 average time/residue: 0.7671 time to fit residues: 586.4685 Evaluate side-chains 625 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 560 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 145 GLN Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain O residue 10 GLN Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 181 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 302 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 350 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 301 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 147 GLN D 146 GLN G 101 ASN H 62 GLN H 71 ASN H 106 GLN H 110 GLN I 153 ASN K 71 ASN L 38 ASN M 160 ASN P 11 ASN S 75 GLN S 226 ASN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS T 80 ASN T 221 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.117029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098883 restraints weight = 43932.526| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.13 r_work: 0.2857 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35494 Z= 0.155 Angle : 0.544 10.761 48065 Z= 0.292 Chirality : 0.042 0.154 5533 Planarity : 0.004 0.055 6190 Dihedral : 4.830 88.587 4979 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.20 % Allowed : 16.26 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 4483 helix: 1.28 (0.11), residues: 2217 sheet: 0.15 (0.18), residues: 780 loop : -1.19 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 226 TYR 0.019 0.001 TYR K 117 PHE 0.015 0.002 PHE J 69 TRP 0.010 0.001 TRP E 100 HIS 0.005 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00367 (35494) covalent geometry : angle 0.54430 (48065) hydrogen bonds : bond 0.04738 ( 2086) hydrogen bonds : angle 4.21641 ( 6108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 595 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8846 (t0) cc_final: 0.8551 (t0) REVERT: B 227 ASP cc_start: 0.7647 (m-30) cc_final: 0.7303 (m-30) REVERT: C 141 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8804 (pttt) REVERT: C 219 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: C 246 LYS cc_start: 0.7269 (mtpt) cc_final: 0.6773 (mmmm) REVERT: D 61 LYS cc_start: 0.8346 (tppp) cc_final: 0.8029 (tptm) REVERT: D 179 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: D 211 MET cc_start: 0.8922 (ttp) cc_final: 0.8680 (ttt) REVERT: D 213 ARG cc_start: 0.5668 (mmp-170) cc_final: 0.3624 (mtm180) REVERT: D 224 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: E 122 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7944 (mm110) REVERT: E 168 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8811 (tpt170) REVERT: E 228 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8422 (ttm) REVERT: E 239 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7802 (ptmt) REVERT: F 16 GLN cc_start: 0.8728 (mp-120) cc_final: 0.8471 (mp10) REVERT: F 86 ASN cc_start: 0.8773 (m110) cc_final: 0.8481 (m-40) REVERT: F 140 MET cc_start: 0.8940 (mmm) cc_final: 0.8684 (mmm) REVERT: F 152 ASN cc_start: 0.8804 (t0) cc_final: 0.8440 (m-40) REVERT: F 185 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7531 (m110) REVERT: G 238 TYR cc_start: 0.8518 (t80) cc_final: 0.8252 (t80) REVERT: H 71 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8413 (t0) REVERT: H 92 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: H 196 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8144 (mmtt) REVERT: I 195 LYS cc_start: 0.6359 (mmtt) cc_final: 0.4593 (tttt) REVERT: I 216 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8669 (mm) REVERT: J 27 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8873 (ttt180) REVERT: J 159 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7921 (p0) REVERT: K 27 GLN cc_start: 0.8456 (mt0) cc_final: 0.7593 (pp30) REVERT: L 141 ARG cc_start: 0.8451 (mmp-170) cc_final: 0.7312 (mtt180) REVERT: M 105 TYR cc_start: 0.8963 (t80) cc_final: 0.8692 (t80) REVERT: M 131 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: M 144 MET cc_start: 0.9086 (mtt) cc_final: 0.8825 (mtm) REVERT: N 5 MET cc_start: 0.8948 (mmm) cc_final: 0.8716 (tpp) REVERT: N 73 ASP cc_start: 0.8327 (m-30) cc_final: 0.7816 (m-30) REVERT: N 186 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8359 (mtm180) REVERT: N 206 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: O 41 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8105 (ttpt) REVERT: O 62 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7661 (ptmt) REVERT: O 76 ASP cc_start: 0.8433 (m-30) cc_final: 0.8062 (m-30) REVERT: O 80 ASN cc_start: 0.9097 (m-40) cc_final: 0.8857 (m-40) REVERT: O 119 GLU cc_start: 0.8138 (tp30) cc_final: 0.7740 (tm-30) REVERT: O 124 THR cc_start: 0.8410 (m) cc_final: 0.8193 (m) REVERT: P 147 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8182 (tp30) REVERT: Q 118 ASP cc_start: 0.7619 (t0) cc_final: 0.7281 (m-30) REVERT: R 100 LYS cc_start: 0.8885 (mttm) cc_final: 0.8555 (mtmt) REVERT: R 226 ASN cc_start: 0.6965 (t0) cc_final: 0.6647 (t0) REVERT: S 189 ASP cc_start: 0.8141 (m-30) cc_final: 0.7801 (m-30) REVERT: T 41 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8094 (mmmm) REVERT: T 119 GLU cc_start: 0.7923 (tp30) cc_final: 0.7521 (mt-10) REVERT: U 115 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8443 (mtmt) outliers start: 116 outliers final: 39 residues processed: 658 average time/residue: 0.7576 time to fit residues: 582.8794 Evaluate side-chains 612 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 551 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 185 GLN Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 220 optimal weight: 6.9990 chunk 261 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 69 ASN D 146 GLN D 175 ASN G 101 ASN H 106 GLN I 153 ASN L 38 ASN M 160 ASN P 11 ASN S 34 GLN S 75 GLN S 80 ASN S 226 ASN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN T 221 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095832 restraints weight = 44453.670| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.16 r_work: 0.2814 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 35494 Z= 0.243 Angle : 0.624 12.220 48065 Z= 0.329 Chirality : 0.046 0.164 5533 Planarity : 0.005 0.054 6190 Dihedral : 5.021 82.275 4979 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.75 % Allowed : 16.89 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.13), residues: 4483 helix: 1.23 (0.11), residues: 2217 sheet: 0.19 (0.18), residues: 769 loop : -1.18 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 226 TYR 0.020 0.002 TYR K 117 PHE 0.020 0.002 PHE J 69 TRP 0.015 0.002 TRP H 103 HIS 0.006 0.001 HIS P 79 Details of bonding type rmsd covalent geometry : bond 0.00592 (35494) covalent geometry : angle 0.62353 (48065) hydrogen bonds : bond 0.05534 ( 2086) hydrogen bonds : angle 4.33872 ( 6108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 564 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7376 (mp) REVERT: A 100 ASN cc_start: 0.8872 (t0) cc_final: 0.8571 (t0) REVERT: B 227 ASP cc_start: 0.7696 (m-30) cc_final: 0.7352 (m-30) REVERT: C 141 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8839 (pttt) REVERT: C 219 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: D 54 GLN cc_start: 0.8974 (tt0) cc_final: 0.8772 (tt0) REVERT: D 179 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6873 (mm-30) REVERT: D 211 MET cc_start: 0.8956 (ttp) cc_final: 0.8721 (ttt) REVERT: D 213 ARG cc_start: 0.5764 (mmp-170) cc_final: 0.3613 (mtm180) REVERT: D 224 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: E 122 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8124 (mm110) REVERT: E 168 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8853 (tpt170) REVERT: E 228 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8436 (ttm) REVERT: E 239 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7813 (ptmt) REVERT: F 86 ASN cc_start: 0.8820 (m110) cc_final: 0.8521 (m-40) REVERT: F 185 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7573 (m110) REVERT: G 238 TYR cc_start: 0.8595 (t80) cc_final: 0.8374 (t80) REVERT: H 71 ASN cc_start: 0.8608 (t0) cc_final: 0.8390 (t0) REVERT: H 92 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: H 196 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8190 (mmtt) REVERT: I 195 LYS cc_start: 0.6385 (mmtt) cc_final: 0.4578 (tttt) REVERT: I 216 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8713 (mm) REVERT: J 159 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7987 (p0) REVERT: K 27 GLN cc_start: 0.8489 (mt0) cc_final: 0.7624 (pp30) REVERT: L 100 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8999 (mtt) REVERT: L 141 ARG cc_start: 0.8517 (mmp-170) cc_final: 0.7320 (mtt180) REVERT: M 39 ASP cc_start: 0.8693 (t0) cc_final: 0.8453 (t0) REVERT: M 105 TYR cc_start: 0.8979 (t80) cc_final: 0.8731 (t80) REVERT: M 131 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7973 (tp40) REVERT: M 144 MET cc_start: 0.9114 (mtt) cc_final: 0.8868 (mtm) REVERT: N 73 ASP cc_start: 0.8373 (m-30) cc_final: 0.7857 (m-30) REVERT: N 206 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: O 76 ASP cc_start: 0.8513 (m-30) cc_final: 0.8151 (m-30) REVERT: O 80 ASN cc_start: 0.9123 (m-40) cc_final: 0.8883 (m-40) REVERT: O 119 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: O 124 THR cc_start: 0.8546 (m) cc_final: 0.8320 (m) REVERT: P 147 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: P 189 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7724 (t0) REVERT: Q 76 ASP cc_start: 0.8644 (m-30) cc_final: 0.8243 (m-30) REVERT: Q 118 ASP cc_start: 0.7565 (t0) cc_final: 0.7228 (m-30) REVERT: R 72 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8463 (mm-40) REVERT: R 100 LYS cc_start: 0.8929 (mttm) cc_final: 0.8588 (mtmt) REVERT: T 41 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8099 (mmmm) REVERT: T 119 GLU cc_start: 0.8115 (tp30) cc_final: 0.7682 (mt-10) REVERT: U 115 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8496 (mtmt) outliers start: 136 outliers final: 62 residues processed: 648 average time/residue: 0.7600 time to fit residues: 574.7546 Evaluate side-chains 621 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 537 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 189 ASP Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 157 ASP Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 380 optimal weight: 9.9990 chunk 307 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 365 optimal weight: 0.9990 chunk 397 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN D 146 GLN G 101 ASN H 106 GLN I 153 ASN K 71 ASN L 29 GLN L 38 ASN L 162 GLN M 146 GLN M 160 ASN P 11 ASN S 34 GLN S 84 GLN S 226 ASN T 34 GLN T 80 ASN T 221 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.120010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101834 restraints weight = 43457.034| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.13 r_work: 0.2870 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35494 Z= 0.124 Angle : 0.512 10.475 48065 Z= 0.274 Chirality : 0.041 0.167 5533 Planarity : 0.004 0.053 6190 Dihedral : 4.607 75.964 4979 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.22 % Allowed : 17.64 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 4483 helix: 1.66 (0.11), residues: 2213 sheet: 0.37 (0.18), residues: 765 loop : -1.02 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 40 TYR 0.017 0.001 TYR K 117 PHE 0.016 0.001 PHE J 69 TRP 0.011 0.001 TRP L 55 HIS 0.005 0.001 HIS F 65 Details of bonding type rmsd covalent geometry : bond 0.00283 (35494) covalent geometry : angle 0.51193 (48065) hydrogen bonds : bond 0.04304 ( 2086) hydrogen bonds : angle 4.06604 ( 6108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 573 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8487 (mtpp) REVERT: B 184 GLU cc_start: 0.7766 (mp0) cc_final: 0.7116 (mp0) REVERT: B 227 ASP cc_start: 0.7670 (m-30) cc_final: 0.7316 (m-30) REVERT: C 219 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: D 61 LYS cc_start: 0.8296 (tppp) cc_final: 0.7987 (tttt) REVERT: D 179 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6984 (mm-30) REVERT: D 211 MET cc_start: 0.8919 (ttp) cc_final: 0.8654 (ttt) REVERT: D 213 ARG cc_start: 0.5401 (mmp-170) cc_final: 0.3480 (mtm180) REVERT: E 122 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8126 (mm110) REVERT: E 168 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8768 (tpp-160) REVERT: E 228 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8404 (ttm) REVERT: E 239 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7780 (ptmt) REVERT: F 86 ASN cc_start: 0.8781 (m110) cc_final: 0.8478 (m-40) REVERT: F 152 ASN cc_start: 0.8829 (t0) cc_final: 0.8497 (m-40) REVERT: G 238 TYR cc_start: 0.8523 (t80) cc_final: 0.8282 (t80) REVERT: H 9 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: H 71 ASN cc_start: 0.8596 (t0) cc_final: 0.8257 (t0) REVERT: H 85 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8443 (mm-30) REVERT: H 92 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: H 165 GLU cc_start: 0.7760 (tt0) cc_final: 0.7527 (tt0) REVERT: H 196 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8172 (mmtt) REVERT: I 195 LYS cc_start: 0.6173 (mmtt) cc_final: 0.4439 (tttt) REVERT: I 216 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8662 (mm) REVERT: J 159 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7834 (p0) REVERT: K 27 GLN cc_start: 0.8410 (mt0) cc_final: 0.7498 (pp30) REVERT: L 141 ARG cc_start: 0.8466 (mmp-170) cc_final: 0.7195 (mtt180) REVERT: M 39 ASP cc_start: 0.8454 (t0) cc_final: 0.8221 (t0) REVERT: M 105 TYR cc_start: 0.8963 (t80) cc_final: 0.8710 (t80) REVERT: M 131 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7766 (tp40) REVERT: M 144 MET cc_start: 0.9092 (mtt) cc_final: 0.8817 (mtm) REVERT: M 170 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8177 (mmm160) REVERT: N 73 ASP cc_start: 0.8325 (m-30) cc_final: 0.7796 (m-30) REVERT: N 206 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: O 41 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8131 (ttpt) REVERT: O 76 ASP cc_start: 0.8454 (m-30) cc_final: 0.8072 (m-30) REVERT: O 80 ASN cc_start: 0.9035 (m-40) cc_final: 0.8765 (m-40) REVERT: O 119 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: Q 212 TYR cc_start: 0.9118 (t80) cc_final: 0.8895 (t80) REVERT: R 72 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8363 (mm-40) REVERT: R 100 LYS cc_start: 0.8886 (mttm) cc_final: 0.8531 (mtmt) REVERT: R 226 ASN cc_start: 0.7030 (t0) cc_final: 0.6705 (t0) REVERT: S 101 GLU cc_start: 0.6002 (mp0) cc_final: 0.5522 (mp0) REVERT: S 189 ASP cc_start: 0.8096 (m-30) cc_final: 0.7698 (m-30) REVERT: T 41 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8131 (mmpt) REVERT: T 65 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: T 119 GLU cc_start: 0.7991 (tp30) cc_final: 0.7481 (mt-10) REVERT: U 115 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8386 (mtmt) outliers start: 117 outliers final: 52 residues processed: 646 average time/residue: 0.8037 time to fit residues: 607.6860 Evaluate side-chains 616 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 544 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 170 ARG Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 265 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 392 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 364 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 146 GLN D 175 ASN G 101 ASN H 106 GLN I 153 ASN L 38 ASN M 160 ASN O 200 HIS Q 210 ASN S 34 GLN S 226 ASN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN T 221 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.116777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098549 restraints weight = 44075.239| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.15 r_work: 0.2859 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35494 Z= 0.149 Angle : 0.533 10.576 48065 Z= 0.284 Chirality : 0.042 0.160 5533 Planarity : 0.004 0.052 6190 Dihedral : 4.612 74.835 4979 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.09 % Allowed : 18.10 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.13), residues: 4483 helix: 1.72 (0.11), residues: 2222 sheet: 0.37 (0.18), residues: 776 loop : -0.95 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 186 TYR 0.018 0.001 TYR K 117 PHE 0.019 0.002 PHE J 69 TRP 0.010 0.001 TRP E 100 HIS 0.005 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00353 (35494) covalent geometry : angle 0.53306 (48065) hydrogen bonds : bond 0.04535 ( 2086) hydrogen bonds : angle 4.06981 ( 6108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 558 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 170 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8838 (mtmt) REVERT: B 184 GLU cc_start: 0.7703 (mp0) cc_final: 0.7095 (mp0) REVERT: B 227 ASP cc_start: 0.7734 (m-30) cc_final: 0.7361 (m-30) REVERT: C 141 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8811 (pttt) REVERT: C 219 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: D 61 LYS cc_start: 0.8336 (tppp) cc_final: 0.8070 (tttt) REVERT: D 179 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: D 211 MET cc_start: 0.8923 (ttp) cc_final: 0.8680 (ttt) REVERT: D 213 ARG cc_start: 0.5682 (mmp-170) cc_final: 0.3659 (mtm180) REVERT: E 119 LEU cc_start: 0.8610 (mt) cc_final: 0.8258 (tp) REVERT: E 122 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8189 (mm110) REVERT: E 168 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8819 (tpp-160) REVERT: E 228 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8416 (ttm) REVERT: E 239 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7749 (ptmt) REVERT: F 185 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7590 (m110) REVERT: G 238 TYR cc_start: 0.8566 (t80) cc_final: 0.8334 (t80) REVERT: H 71 ASN cc_start: 0.8631 (t0) cc_final: 0.8367 (t0) REVERT: H 92 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: H 165 GLU cc_start: 0.7806 (tt0) cc_final: 0.7579 (tt0) REVERT: H 196 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8162 (mmtt) REVERT: I 195 LYS cc_start: 0.6303 (mmtt) cc_final: 0.4549 (tttt) REVERT: I 216 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8692 (mm) REVERT: J 159 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7792 (p0) REVERT: K 27 GLN cc_start: 0.8421 (mt0) cc_final: 0.7601 (pp30) REVERT: L 141 ARG cc_start: 0.8497 (mmp-170) cc_final: 0.7279 (mtt180) REVERT: M 39 ASP cc_start: 0.8632 (t0) cc_final: 0.8424 (t0) REVERT: M 105 TYR cc_start: 0.8962 (t80) cc_final: 0.8709 (t80) REVERT: M 131 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7812 (tp40) REVERT: M 144 MET cc_start: 0.9089 (mtt) cc_final: 0.8836 (mtm) REVERT: N 73 ASP cc_start: 0.8322 (m-30) cc_final: 0.7781 (m-30) REVERT: N 206 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: O 41 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8174 (ttpt) REVERT: O 76 ASP cc_start: 0.8460 (m-30) cc_final: 0.8094 (m-30) REVERT: O 80 ASN cc_start: 0.9075 (m-40) cc_final: 0.8818 (m-40) REVERT: O 119 GLU cc_start: 0.8161 (tp30) cc_final: 0.7794 (tm-30) REVERT: R 72 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8382 (mm-40) REVERT: R 100 LYS cc_start: 0.8897 (mttm) cc_final: 0.8571 (mtmt) REVERT: R 182 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: S 189 ASP cc_start: 0.8111 (m-30) cc_final: 0.7711 (m-30) REVERT: T 65 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: T 119 GLU cc_start: 0.8073 (tp30) cc_final: 0.7594 (mt-10) REVERT: U 57 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7518 (ttp-170) REVERT: U 115 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8488 (mtmt) outliers start: 112 outliers final: 68 residues processed: 624 average time/residue: 0.7742 time to fit residues: 566.3185 Evaluate side-chains 628 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 541 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain Q residue 224 THR Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 277 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 297 optimal weight: 0.9980 chunk 300 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 369 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 146 GLN G 101 ASN H 106 GLN I 153 ASN K 71 ASN L 38 ASN M 160 ASN N 208 ASN P 11 ASN Q 210 ASN S 34 GLN S 226 ASN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN T 221 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.115685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.096959 restraints weight = 44272.117| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.15 r_work: 0.2842 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35494 Z= 0.174 Angle : 0.559 11.094 48065 Z= 0.296 Chirality : 0.043 0.162 5533 Planarity : 0.004 0.052 6190 Dihedral : 4.712 76.427 4979 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.36 % Allowed : 18.21 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.13), residues: 4483 helix: 1.67 (0.11), residues: 2223 sheet: 0.39 (0.18), residues: 776 loop : -0.95 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 186 TYR 0.019 0.001 TYR K 117 PHE 0.020 0.002 PHE J 69 TRP 0.011 0.001 TRP H 103 HIS 0.005 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00419 (35494) covalent geometry : angle 0.55873 (48065) hydrogen bonds : bond 0.04821 ( 2086) hydrogen bonds : angle 4.13237 ( 6108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 545 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8833 (t0) cc_final: 0.8606 (t0) REVERT: B 184 GLU cc_start: 0.7766 (mp0) cc_final: 0.7124 (mp0) REVERT: B 227 ASP cc_start: 0.7779 (m-30) cc_final: 0.7407 (m-30) REVERT: C 141 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8827 (pttt) REVERT: C 219 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: D 179 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7000 (mm-30) REVERT: D 211 MET cc_start: 0.8926 (ttp) cc_final: 0.8669 (ttt) REVERT: D 213 ARG cc_start: 0.5569 (mmp-170) cc_final: 0.3410 (mtm180) REVERT: E 59 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8733 (ptp) REVERT: E 119 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8361 (tp) REVERT: E 168 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8858 (tpp-160) REVERT: E 228 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8433 (ttm) REVERT: E 239 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7691 (ptmt) REVERT: F 185 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7608 (m110) REVERT: G 238 TYR cc_start: 0.8563 (t80) cc_final: 0.8353 (t80) REVERT: H 71 ASN cc_start: 0.8625 (t0) cc_final: 0.8372 (t0) REVERT: H 92 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: H 165 GLU cc_start: 0.7829 (tt0) cc_final: 0.7596 (tt0) REVERT: H 196 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8181 (mmtt) REVERT: I 195 LYS cc_start: 0.6359 (mmtt) cc_final: 0.4549 (tttt) REVERT: I 216 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8707 (mm) REVERT: J 159 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7848 (p0) REVERT: K 27 GLN cc_start: 0.8432 (mt0) cc_final: 0.7597 (pp30) REVERT: L 141 ARG cc_start: 0.8479 (mmp-170) cc_final: 0.7344 (mtt180) REVERT: M 39 ASP cc_start: 0.8660 (t0) cc_final: 0.8429 (t0) REVERT: M 105 TYR cc_start: 0.8965 (t80) cc_final: 0.8708 (t80) REVERT: M 131 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7823 (tp40) REVERT: M 144 MET cc_start: 0.9102 (mtt) cc_final: 0.8856 (mtm) REVERT: N 73 ASP cc_start: 0.8312 (m-30) cc_final: 0.7766 (m-30) REVERT: N 186 ARG cc_start: 0.8658 (mtp180) cc_final: 0.8444 (mtm180) REVERT: N 206 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: O 62 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7616 (ptmt) REVERT: O 76 ASP cc_start: 0.8469 (m-30) cc_final: 0.8112 (m-30) REVERT: O 80 ASN cc_start: 0.9081 (m-40) cc_final: 0.8828 (m-40) REVERT: O 119 GLU cc_start: 0.8168 (tp30) cc_final: 0.7837 (tm-30) REVERT: R 72 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8485 (mm-40) REVERT: R 100 LYS cc_start: 0.8903 (mttm) cc_final: 0.8573 (mtmt) REVERT: R 182 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: S 101 GLU cc_start: 0.6240 (mp0) cc_final: 0.5736 (mp0) REVERT: S 189 ASP cc_start: 0.8124 (m-30) cc_final: 0.7724 (m-30) REVERT: T 119 GLU cc_start: 0.8155 (tp30) cc_final: 0.7585 (mt-10) REVERT: U 14 ASP cc_start: 0.7822 (m-30) cc_final: 0.7535 (m-30) REVERT: U 57 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7503 (ttp-170) REVERT: U 115 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8451 (mtmt) outliers start: 122 outliers final: 74 residues processed: 618 average time/residue: 0.7735 time to fit residues: 559.9504 Evaluate side-chains 628 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 535 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain Q residue 224 THR Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 147 GLU Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 355 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 433 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 377 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.0050 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 155 ASN D 146 GLN D 175 ASN G 101 ASN H 106 GLN I 153 ASN L 38 ASN M 160 ASN P 11 ASN Q 210 ASN S 34 GLN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN T 221 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.116899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098966 restraints weight = 44054.544| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.14 r_work: 0.2856 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35494 Z= 0.140 Angle : 0.526 10.485 48065 Z= 0.281 Chirality : 0.042 0.163 5533 Planarity : 0.004 0.052 6190 Dihedral : 4.568 74.130 4979 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.98 % Allowed : 18.82 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4483 helix: 1.79 (0.11), residues: 2218 sheet: 0.48 (0.18), residues: 771 loop : -0.90 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 89 TYR 0.018 0.001 TYR K 117 PHE 0.018 0.001 PHE J 69 TRP 0.011 0.001 TRP L 55 HIS 0.004 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00329 (35494) covalent geometry : angle 0.52628 (48065) hydrogen bonds : bond 0.04415 ( 2086) hydrogen bonds : angle 4.04263 ( 6108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 555 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8834 (t0) cc_final: 0.8607 (t0) REVERT: B 112 ARG cc_start: 0.8989 (mtt-85) cc_final: 0.8671 (mtt90) REVERT: B 227 ASP cc_start: 0.7766 (m-30) cc_final: 0.7374 (m-30) REVERT: C 141 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8809 (pttt) REVERT: C 219 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: D 61 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8091 (tptm) REVERT: D 179 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: D 211 MET cc_start: 0.8930 (ttp) cc_final: 0.8690 (ttt) REVERT: D 213 ARG cc_start: 0.5612 (mmp-170) cc_final: 0.3454 (mtm180) REVERT: E 59 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8737 (ptp) REVERT: E 119 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8334 (tp) REVERT: E 168 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8821 (tpp-160) REVERT: E 228 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8434 (ttm) REVERT: E 239 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7872 (pttt) REVERT: F 185 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7593 (m110) REVERT: G 238 TYR cc_start: 0.8567 (t80) cc_final: 0.8347 (t80) REVERT: H 71 ASN cc_start: 0.8608 (t0) cc_final: 0.8380 (t0) REVERT: H 92 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: H 165 GLU cc_start: 0.7813 (tt0) cc_final: 0.7575 (tt0) REVERT: H 196 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8146 (mmtt) REVERT: I 195 LYS cc_start: 0.6173 (mmtt) cc_final: 0.4407 (tttt) REVERT: I 216 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8693 (mm) REVERT: J 159 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7759 (p0) REVERT: K 27 GLN cc_start: 0.8422 (mt0) cc_final: 0.7567 (pp30) REVERT: L 141 ARG cc_start: 0.8475 (mmp-170) cc_final: 0.7315 (mtt180) REVERT: M 39 ASP cc_start: 0.8633 (t0) cc_final: 0.8412 (t0) REVERT: M 105 TYR cc_start: 0.8960 (t80) cc_final: 0.8700 (t80) REVERT: M 131 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7792 (tp40) REVERT: M 144 MET cc_start: 0.9110 (mtt) cc_final: 0.8856 (mtm) REVERT: N 73 ASP cc_start: 0.8292 (m-30) cc_final: 0.7775 (m-30) REVERT: N 186 ARG cc_start: 0.8626 (mtp180) cc_final: 0.8415 (mtm180) REVERT: N 206 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: O 41 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8209 (ttpt) REVERT: O 76 ASP cc_start: 0.8454 (m-30) cc_final: 0.8108 (m-30) REVERT: O 80 ASN cc_start: 0.9078 (m-40) cc_final: 0.8825 (m-40) REVERT: O 119 GLU cc_start: 0.8165 (tp30) cc_final: 0.7846 (tm-30) REVERT: P 189 ASP cc_start: 0.8145 (m-30) cc_final: 0.7668 (t0) REVERT: Q 65 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6770 (tm-30) REVERT: R 72 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8419 (mm-40) REVERT: R 100 LYS cc_start: 0.8883 (mttm) cc_final: 0.8562 (mtmt) REVERT: R 182 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7023 (mm-30) REVERT: S 101 GLU cc_start: 0.6159 (mp0) cc_final: 0.5667 (mp0) REVERT: S 189 ASP cc_start: 0.8123 (m-30) cc_final: 0.7729 (m-30) REVERT: T 119 GLU cc_start: 0.8079 (tp30) cc_final: 0.7589 (mt-10) REVERT: U 57 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7510 (ttp-170) REVERT: U 115 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8467 (mtmt) outliers start: 108 outliers final: 75 residues processed: 618 average time/residue: 0.7820 time to fit residues: 566.4818 Evaluate side-chains 632 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 537 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain Q residue 224 THR Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 147 GLU Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 127 optimal weight: 0.9990 chunk 331 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 393 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN C 69 ASN D 146 GLN G 101 ASN H 106 GLN I 153 ASN K 71 ASN L 38 ASN M 160 ASN Q 210 ASN S 34 GLN S 226 ASN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN T 221 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.116624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.098419 restraints weight = 44279.738| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.15 r_work: 0.2855 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35494 Z= 0.148 Angle : 0.539 10.506 48065 Z= 0.286 Chirality : 0.042 0.160 5533 Planarity : 0.004 0.052 6190 Dihedral : 4.584 73.801 4979 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.89 % Allowed : 19.15 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4483 helix: 1.81 (0.11), residues: 2222 sheet: 0.46 (0.18), residues: 776 loop : -0.85 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 186 TYR 0.018 0.001 TYR K 117 PHE 0.019 0.002 PHE J 69 TRP 0.011 0.001 TRP H 103 HIS 0.004 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00352 (35494) covalent geometry : angle 0.53911 (48065) hydrogen bonds : bond 0.04509 ( 2086) hydrogen bonds : angle 4.05741 ( 6108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 551 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8838 (t0) cc_final: 0.8609 (t0) REVERT: B 112 ARG cc_start: 0.9017 (mtt-85) cc_final: 0.8722 (mtt90) REVERT: B 227 ASP cc_start: 0.7814 (m-30) cc_final: 0.7414 (m-30) REVERT: C 141 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8822 (pttt) REVERT: C 219 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: D 61 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8110 (tptm) REVERT: D 179 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: D 211 MET cc_start: 0.8910 (ttp) cc_final: 0.8667 (ttt) REVERT: D 213 ARG cc_start: 0.5618 (mmp-170) cc_final: 0.3437 (mtm180) REVERT: E 59 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8740 (ptp) REVERT: E 119 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8419 (tp) REVERT: E 168 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8821 (tpp-160) REVERT: E 228 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8442 (ttm) REVERT: F 185 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7607 (m110) REVERT: G 238 TYR cc_start: 0.8565 (t80) cc_final: 0.8354 (t80) REVERT: H 71 ASN cc_start: 0.8603 (t0) cc_final: 0.8371 (t0) REVERT: H 92 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: H 165 GLU cc_start: 0.7806 (tt0) cc_final: 0.7598 (tt0) REVERT: H 196 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8161 (mmtt) REVERT: I 195 LYS cc_start: 0.6058 (mmtt) cc_final: 0.4400 (tttt) REVERT: I 216 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8696 (mm) REVERT: J 159 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7750 (p0) REVERT: K 27 GLN cc_start: 0.8421 (mt0) cc_final: 0.7579 (pp30) REVERT: L 141 ARG cc_start: 0.8490 (mmp-170) cc_final: 0.7326 (mtt180) REVERT: M 39 ASP cc_start: 0.8641 (t0) cc_final: 0.8415 (t0) REVERT: M 105 TYR cc_start: 0.8970 (t80) cc_final: 0.8704 (t80) REVERT: M 131 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7783 (tp40) REVERT: M 144 MET cc_start: 0.9111 (mtt) cc_final: 0.8862 (mtm) REVERT: N 73 ASP cc_start: 0.8337 (m-30) cc_final: 0.7811 (m-30) REVERT: N 206 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7043 (pm20) REVERT: O 41 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8229 (ttpt) REVERT: O 76 ASP cc_start: 0.8461 (m-30) cc_final: 0.8120 (m-30) REVERT: O 80 ASN cc_start: 0.9078 (m-40) cc_final: 0.8831 (m-40) REVERT: O 119 GLU cc_start: 0.8184 (tp30) cc_final: 0.7862 (tm-30) REVERT: P 189 ASP cc_start: 0.8151 (m-30) cc_final: 0.7669 (t0) REVERT: R 72 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8381 (mm-40) REVERT: R 100 LYS cc_start: 0.8891 (mttm) cc_final: 0.8566 (mtmt) REVERT: S 189 ASP cc_start: 0.8137 (m-30) cc_final: 0.7743 (m-30) REVERT: T 119 GLU cc_start: 0.8165 (tp30) cc_final: 0.7590 (mt-10) REVERT: U 57 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7496 (ttp-170) REVERT: U 115 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8488 (mtmt) outliers start: 105 outliers final: 74 residues processed: 610 average time/residue: 0.7738 time to fit residues: 553.0440 Evaluate side-chains 639 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 547 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain Q residue 224 THR Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 147 GLU Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 20 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 375 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 331 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 69 ASN D 146 GLN G 101 ASN H 106 GLN I 153 ASN L 38 ASN M 77 HIS M 160 ASN P 11 ASN Q 210 ASN S 34 GLN S 226 ASN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN T 221 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.096046 restraints weight = 44273.144| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.15 r_work: 0.2818 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 35494 Z= 0.231 Angle : 0.614 11.856 48065 Z= 0.324 Chirality : 0.045 0.168 5533 Planarity : 0.005 0.052 6190 Dihedral : 4.877 79.386 4979 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.20 % Allowed : 18.96 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.13), residues: 4483 helix: 1.56 (0.11), residues: 2217 sheet: 0.41 (0.18), residues: 774 loop : -0.97 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 9 TYR 0.021 0.002 TYR K 117 PHE 0.021 0.002 PHE J 69 TRP 0.015 0.002 TRP H 103 HIS 0.005 0.001 HIS P 79 Details of bonding type rmsd covalent geometry : bond 0.00565 (35494) covalent geometry : angle 0.61434 (48065) hydrogen bonds : bond 0.05322 ( 2086) hydrogen bonds : angle 4.24326 ( 6108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12673.94 seconds wall clock time: 215 minutes 55.35 seconds (12955.35 seconds total)