Starting phenix.real_space_refine on Tue Aug 26 21:18:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a0q_2981/08_2025/5a0q_2981.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a0q_2981/08_2025/5a0q_2981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5a0q_2981/08_2025/5a0q_2981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a0q_2981/08_2025/5a0q_2981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5a0q_2981/08_2025/5a0q_2981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a0q_2981/08_2025/5a0q_2981.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 284 5.16 5 C 27550 2.51 5 N 7448 2.21 5 O 8166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43448 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1860 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1674 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1535 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 3 Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1626 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 5, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1490 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1374 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1512 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1480 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1453 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1428 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1860 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1674 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1535 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 3 Chain: "U" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1626 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 5, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1490 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 1 Chain: "X" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1374 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1512 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1480 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1453 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "b" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1428 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 15 Chain: "V" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 15 Chain: "W" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 8.37, per 1000 atoms: 0.19 Number of scatterers: 43448 At special positions: 0 Unit cell: (132.08, 171.6, 134.16, 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 284 16.00 O 8166 8.00 N 7448 7.00 C 27550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 61 " distance=2.01 Simple disulfide: pdb=" SG CYS a 54 " - pdb=" SG CYS a 61 " distance=2.01 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10256 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 0 sheets defined 35.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 84 through 105 removed outlier: 4.026A pdb=" N ARG A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.840A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.990A pdb=" N PHE A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 79 through 100 removed outlier: 3.788A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 4.147A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.095A pdb=" N THR B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.760A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.679A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C 29 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 101 Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.845A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 4.262A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 230 through 243 removed outlier: 3.719A pdb=" N GLU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.732A pdb=" N LYS D 27 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 removed outlier: 4.639A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.994A pdb=" N TYR D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 185 through 198 removed outlier: 4.060A pdb=" N LEU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 234 removed outlier: 4.565A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU D 233 " --> pdb=" O VAL D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.937A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 103 removed outlier: 4.008A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.775A pdb=" N VAL E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.852A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.513A pdb=" N SER E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN E 204 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.596A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 231 through 235' Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.777A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 98 removed outlier: 3.774A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 121 removed outlier: 4.206A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.904A pdb=" N LEU F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU F 173 " --> pdb=" O ARG F 169 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG F 174 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 196 removed outlier: 3.681A pdb=" N ARG F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.847A pdb=" N ALA G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 102 removed outlier: 4.122A pdb=" N SER G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.893A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR G 122 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU G 124 " --> pdb=" O HIS G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 186 through 200 removed outlier: 4.550A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'H' and resid 49 through 54 removed outlier: 3.764A pdb=" N ALA H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 70 removed outlier: 3.537A pdb=" N ILE H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 89 Processing helix chain 'H' and resid 132 through 140 removed outlier: 4.117A pdb=" N TYR H 136 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR H 138 " --> pdb=" O TYR H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 166 removed outlier: 4.225A pdb=" N LEU H 153 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU H 162 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 89 Processing helix chain 'I' and resid 130 through 141 removed outlier: 3.808A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 165 removed outlier: 4.510A pdb=" N LYS I 152 " --> pdb=" O GLU I 148 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN I 153 " --> pdb=" O GLU I 149 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER I 156 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU I 157 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA I 158 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 76 removed outlier: 3.577A pdb=" N TYR J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 96 Processing helix chain 'J' and resid 159 through 176 removed outlier: 4.025A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG J 176 " --> pdb=" O ASN J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 71 removed outlier: 3.847A pdb=" N TYR K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN K 63 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS K 68 " --> pdb=" O VAL K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 93 removed outlier: 3.957A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 146 removed outlier: 5.303A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 170 removed outlier: 3.541A pdb=" N VAL K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU K 158 " --> pdb=" O GLU K 154 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 70 removed outlier: 3.577A pdb=" N SER L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.550A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 3.980A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 removed outlier: 4.086A pdb=" N ARG L 166 " --> pdb=" O GLN L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 79 removed outlier: 3.579A pdb=" N THR M 63 " --> pdb=" O GLY M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 98 removed outlier: 4.160A pdb=" N SER M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 168 through 185 removed outlier: 3.824A pdb=" N VAL M 178 " --> pdb=" O LEU M 174 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 76 removed outlier: 3.829A pdb=" N LEU N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 102 removed outlier: 3.667A pdb=" N LYS N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 156 removed outlier: 3.905A pdb=" N VAL N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.057A pdb=" N ARG N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 35 Processing helix chain 'O' and resid 84 through 105 removed outlier: 4.026A pdb=" N ARG O 88 " --> pdb=" O THR O 84 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN O 90 " --> pdb=" O ASP O 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 127 removed outlier: 3.841A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 181 removed outlier: 3.990A pdb=" N PHE O 178 " --> pdb=" O GLU O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 206 Processing helix chain 'O' and resid 212 through 214 No H-bonds generated for 'chain 'O' and resid 212 through 214' Processing helix chain 'P' and resid 19 through 29 Processing helix chain 'P' and resid 79 through 100 removed outlier: 3.788A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS P 87 " --> pdb=" O ARG P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 122 removed outlier: 4.148A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN P 122 " --> pdb=" O GLN P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 removed outlier: 4.093A pdb=" N THR P 171 " --> pdb=" O VAL P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 196 removed outlier: 3.760A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU P 196 " --> pdb=" O LEU P 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 5 No H-bonds generated for 'chain 'Q' and resid 3 through 5' Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.679A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY Q 29 " --> pdb=" O MET Q 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 101 Processing helix chain 'Q' and resid 107 through 123 removed outlier: 3.845A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 178 removed outlier: 4.262A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 200 Processing helix chain 'Q' and resid 230 through 243 removed outlier: 3.719A pdb=" N GLU Q 242 " --> pdb=" O LYS Q 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 28 removed outlier: 3.732A pdb=" N LYS R 27 " --> pdb=" O GLN R 23 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 97 removed outlier: 4.639A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG R 86 " --> pdb=" O ILE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 119 removed outlier: 3.994A pdb=" N TYR R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 Processing helix chain 'R' and resid 185 through 198 removed outlier: 4.060A pdb=" N LEU R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 234 removed outlier: 4.565A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU R 233 " --> pdb=" O VAL R 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 33 removed outlier: 3.937A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 103 removed outlier: 4.008A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 120 removed outlier: 3.775A pdb=" N VAL S 116 " --> pdb=" O VAL S 112 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 184 removed outlier: 3.852A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL S 184 " --> pdb=" O SER S 180 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 205 removed outlier: 3.512A pdb=" N SER S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS S 203 " --> pdb=" O LEU S 199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN S 204 " --> pdb=" O ILE S 200 " (cutoff:3.500A) Processing helix chain 'S' and resid 231 through 235 removed outlier: 3.596A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 231 through 235' Processing helix chain 'T' and resid 20 through 31 removed outlier: 3.777A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN T 31 " --> pdb=" O GLU T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 98 removed outlier: 3.774A pdb=" N GLN T 90 " --> pdb=" O ASN T 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER T 95 " --> pdb=" O GLU T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 121 removed outlier: 4.207A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix Processing helix chain 'T' and resid 165 through 174 removed outlier: 3.904A pdb=" N LEU T 172 " --> pdb=" O ALA T 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG T 174 " --> pdb=" O THR T 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 196 removed outlier: 3.681A pdb=" N ARG T 193 " --> pdb=" O LYS T 189 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 32 removed outlier: 3.848A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 102 removed outlier: 4.122A pdb=" N SER U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 124 removed outlier: 3.893A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR U 122 " --> pdb=" O TYR U 118 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR U 123 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU U 124 " --> pdb=" O HIS U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 178 Processing helix chain 'U' and resid 186 through 200 removed outlier: 4.550A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA U 194 " --> pdb=" O VAL U 190 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 236 Processing helix chain 'V' and resid 49 through 54 removed outlier: 3.764A pdb=" N ALA V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 70 removed outlier: 3.537A pdb=" N ILE V 68 " --> pdb=" O GLY V 64 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU V 69 " --> pdb=" O PHE V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 89 Processing helix chain 'V' and resid 132 through 140 removed outlier: 4.117A pdb=" N TYR V 136 " --> pdb=" O SER V 132 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY V 137 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR V 138 " --> pdb=" O TYR V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 166 removed outlier: 4.225A pdb=" N LEU V 153 " --> pdb=" O LYS V 149 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN V 154 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA V 161 " --> pdb=" O ALA V 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU V 162 " --> pdb=" O ASN V 158 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG V 166 " --> pdb=" O LEU V 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 70 Processing helix chain 'W' and resid 76 through 89 Processing helix chain 'W' and resid 130 through 141 removed outlier: 3.808A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 165 removed outlier: 4.510A pdb=" N LYS W 152 " --> pdb=" O GLU W 148 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN W 153 " --> pdb=" O GLU W 149 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER W 156 " --> pdb=" O LYS W 152 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU W 157 " --> pdb=" O ASN W 153 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA W 158 " --> pdb=" O LEU W 154 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 76 removed outlier: 3.576A pdb=" N TYR X 73 " --> pdb=" O ARG X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 96 Processing helix chain 'X' and resid 159 through 176 removed outlier: 4.025A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG X 176 " --> pdb=" O ASN X 172 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 71 removed outlier: 3.847A pdb=" N TYR Y 59 " --> pdb=" O GLN Y 55 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN Y 63 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS Y 68 " --> pdb=" O VAL Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 93 removed outlier: 3.958A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 146 removed outlier: 5.303A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 170 removed outlier: 3.541A pdb=" N VAL Y 157 " --> pdb=" O ARG Y 153 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU Y 158 " --> pdb=" O GLU Y 154 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS Y 163 " --> pdb=" O LEU Y 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU Y 165 " --> pdb=" O ARG Y 161 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU Y 166 " --> pdb=" O LYS Y 162 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU Y 167 " --> pdb=" O CYS Y 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 70 removed outlier: 3.577A pdb=" N SER Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 90 removed outlier: 3.550A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 142 removed outlier: 3.980A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 166 removed outlier: 4.087A pdb=" N ARG Z 166 " --> pdb=" O GLN Z 162 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 79 removed outlier: 3.579A pdb=" N THR a 63 " --> pdb=" O GLY a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 98 removed outlier: 4.160A pdb=" N SER a 93 " --> pdb=" O ALA a 89 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 168 through 185 removed outlier: 3.823A pdb=" N VAL a 178 " --> pdb=" O LEU a 174 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE a 179 " --> pdb=" O VAL a 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 76 removed outlier: 3.829A pdb=" N LEU b 76 " --> pdb=" O ILE b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 102 removed outlier: 3.667A pdb=" N LYS b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 156 removed outlier: 3.905A pdb=" N VAL b 153 " --> pdb=" O LEU b 149 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 163 through 174 removed outlier: 4.057A pdb=" N ARG b 174 " --> pdb=" O GLU b 170 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3606 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: 5.63 Time building geometry restraints manager: 4.06 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: 9099 1.33 - 1.46: 15127 1.46 - 1.59: 19485 1.59 - 1.72: 13 1.72 - 1.85: 450 Bond restraints: 44174 Sorted by residual: bond pdb=" C THR V 1 " pdb=" N THR V 2 " ideal model delta sigma weight residual 1.331 1.782 -0.451 1.30e-02 5.92e+03 1.20e+03 bond pdb=" C THR H 1 " pdb=" N THR H 2 " ideal model delta sigma weight residual 1.331 1.782 -0.451 1.30e-02 5.92e+03 1.20e+03 bond pdb=" C THR L 1 " pdb=" N THR L 2 " ideal model delta sigma weight residual 1.331 1.485 -0.154 1.37e-02 5.33e+03 1.27e+02 bond pdb=" C THR Z 1 " pdb=" N THR Z 2 " ideal model delta sigma weight residual 1.331 1.485 -0.154 1.37e-02 5.33e+03 1.27e+02 bond pdb=" N PRO I 123 " pdb=" CD PRO I 123 " ideal model delta sigma weight residual 1.473 1.367 0.106 1.40e-02 5.10e+03 5.72e+01 ... (remaining 44169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.68: 59285 7.68 - 15.36: 309 15.36 - 23.03: 25 23.03 - 30.71: 2 30.71 - 38.39: 1 Bond angle restraints: 59622 Sorted by residual: angle pdb=" N GLY T 17 " pdb=" CA GLY T 17 " pdb=" C GLY T 17 " ideal model delta sigma weight residual 113.18 151.57 -38.39 2.37e+00 1.78e-01 2.62e+02 angle pdb=" N SER E 172 " pdb=" CA SER E 172 " pdb=" C SER E 172 " ideal model delta sigma weight residual 111.14 125.87 -14.73 1.08e+00 8.57e-01 1.86e+02 angle pdb=" N SER S 172 " pdb=" CA SER S 172 " pdb=" C SER S 172 " ideal model delta sigma weight residual 111.14 125.81 -14.67 1.08e+00 8.57e-01 1.84e+02 angle pdb=" N SER Q 153 " pdb=" CA SER Q 153 " pdb=" C SER Q 153 " ideal model delta sigma weight residual 108.79 89.26 19.53 1.53e+00 4.27e-01 1.63e+02 angle pdb=" N SER C 153 " pdb=" CA SER C 153 " pdb=" C SER C 153 " ideal model delta sigma weight residual 108.79 89.28 19.51 1.53e+00 4.27e-01 1.63e+02 ... (remaining 59617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.75: 25352 26.75 - 53.49: 949 53.49 - 80.24: 283 80.24 - 106.98: 40 106.98 - 133.73: 8 Dihedral angle restraints: 26632 sinusoidal: 10596 harmonic: 16036 Sorted by residual: dihedral pdb=" CA GLU M 18 " pdb=" C GLU M 18 " pdb=" N ASP M 19 " pdb=" CA ASP M 19 " ideal model delta harmonic sigma weight residual 180.00 -137.66 -42.34 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" CA GLU a 18 " pdb=" C GLU a 18 " pdb=" N ASP a 19 " pdb=" CA ASP a 19 " ideal model delta harmonic sigma weight residual -180.00 -137.66 -42.34 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" C GLN V 7 " pdb=" N GLN V 7 " pdb=" CA GLN V 7 " pdb=" CB GLN V 7 " ideal model delta harmonic sigma weight residual -122.60 -103.78 -18.82 0 2.50e+00 1.60e-01 5.67e+01 ... (remaining 26629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 5441 0.144 - 0.288: 1168 0.288 - 0.433: 102 0.433 - 0.577: 20 0.577 - 0.721: 1 Chirality restraints: 6732 Sorted by residual: chirality pdb=" CA PHE H 8 " pdb=" N PHE H 8 " pdb=" C PHE H 8 " pdb=" CB PHE H 8 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA MET W 135 " pdb=" N MET W 135 " pdb=" C MET W 135 " pdb=" CB MET W 135 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CA MET I 135 " pdb=" N MET I 135 " pdb=" C MET I 135 " pdb=" CB MET I 135 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 6729 not shown) Planarity restraints: 7614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 KNM W 300 " 0.005 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C8 KNM W 300 " -0.068 2.00e-02 2.50e+03 pdb=" C9 KNM W 300 " 0.312 2.00e-02 2.50e+03 pdb=" N2 KNM W 300 " -0.460 2.00e-02 2.50e+03 pdb=" O3 KNM W 300 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 KNM I 300 " -0.005 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C8 KNM I 300 " 0.068 2.00e-02 2.50e+03 pdb=" C9 KNM I 300 " -0.311 2.00e-02 2.50e+03 pdb=" N2 KNM I 300 " 0.460 2.00e-02 2.50e+03 pdb=" O3 KNM I 300 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 KNM H 300 " -0.191 2.00e-02 2.50e+03 2.47e-01 7.65e+02 pdb=" C8 KNM H 300 " 0.082 2.00e-02 2.50e+03 pdb=" C9 KNM H 300 " -0.298 2.00e-02 2.50e+03 pdb=" N2 KNM H 300 " 0.417 2.00e-02 2.50e+03 pdb=" O3 KNM H 300 " -0.010 2.00e-02 2.50e+03 ... (remaining 7611 not shown) Histogram of nonbonded interaction distances: 0.70 - 1.54: 8 1.54 - 2.38: 298 2.38 - 3.22: 44308 3.22 - 4.06: 114887 4.06 - 4.90: 213821 Warning: very small nonbonded interaction distances. Nonbonded interactions: 373322 Sorted by model distance: nonbonded pdb=" O SER Y 23 " pdb=" OD1 ASN Y 24 " model vdw 0.702 3.040 nonbonded pdb=" O SER K 23 " pdb=" OD1 ASN K 24 " model vdw 0.702 3.040 nonbonded pdb=" O VAL X 137 " pdb=" OH TYR X 146 " model vdw 0.977 3.040 nonbonded pdb=" O VAL J 137 " pdb=" OH TYR J 146 " model vdw 0.977 3.040 nonbonded pdb=" ND2 ASN V 28 " pdb=" OG1 THR V 31 " model vdw 1.432 3.120 ... (remaining 373317 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 32.050 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 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 : 0.020 0.451 44190 Z= 1.413 Angle : 2.216 38.391 59626 Z= 1.459 Chirality : 0.115 0.721 6732 Planarity : 0.019 0.267 7614 Dihedral : 16.221 133.728 16370 Min Nonbonded Distance : 0.702 Molprobity Statistics. All-atom Clashscore : 33.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.46 % Favored : 95.14 % Rotamer: Outliers : 1.99 % Allowed : 9.50 % Favored : 88.51 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -3.18 (0.09), residues: 5432 helix: -2.12 (0.08), residues: 1892 sheet: -2.40 (0.13), residues: 1204 loop : -1.71 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 129 TYR 0.135 0.018 TYR M 188 PHE 0.115 0.015 PHE Z 6 TRP 0.105 0.015 TRP V 103 HIS 0.008 0.001 HIS T 43 Details of bonding type rmsd covalent geometry : bond 0.01928 (44174) covalent geometry : angle 2.21575 (59622) SS BOND : bond 0.02364 ( 2) SS BOND : angle 4.12377 ( 4) hydrogen bonds : bond 0.19765 ( 1202) hydrogen bonds : angle 8.40085 ( 3606) Misc. bond : bond 0.23237 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1964 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1872 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR J 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR X 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7694 (mt) cc_final: 0.7369 (mt) REVERT: B 51 GLN cc_start: 0.3953 (OUTLIER) cc_final: 0.2828 (pp30) REVERT: B 207 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.5213 (pp) REVERT: B 213 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6249 (m-40) REVERT: D 153 TYR cc_start: 0.7334 (p90) cc_final: 0.7116 (p90) REVERT: E 21 LEU cc_start: 0.6569 (mt) cc_final: 0.6313 (mp) REVERT: E 70 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8326 (mm) REVERT: E 97 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8167 (mm110) REVERT: H 186 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5123 (mtt180) REVERT: I 126 THR cc_start: 0.8572 (p) cc_final: 0.8157 (m) REVERT: I 139 GLU cc_start: 0.5315 (tt0) cc_final: 0.5106 (tt0) REVERT: J 134 ASP cc_start: 0.5606 (p0) cc_final: 0.5214 (p0) REVERT: J 170 MET cc_start: 0.7280 (tpt) cc_final: 0.7007 (tpt) REVERT: K 14 LEU cc_start: 0.7694 (tp) cc_final: 0.7233 (tt) REVERT: M 15 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.5142 (pt) REVERT: M 28 ARG cc_start: 0.5771 (ptt180) cc_final: 0.5282 (ptm160) REVERT: M 72 LEU cc_start: 0.7819 (pp) cc_final: 0.7538 (pp) REVERT: M 74 MET cc_start: 0.6047 (mtt) cc_final: 0.5772 (mtp) REVERT: M 173 ARG cc_start: 0.4914 (tpp-160) cc_final: 0.4587 (mtp85) REVERT: N 199 ILE cc_start: 0.5885 (mt) cc_final: 0.5662 (mp) REVERT: O 32 ILE cc_start: 0.7672 (mt) cc_final: 0.7345 (mt) REVERT: O 104 LYS cc_start: 0.7686 (mtpt) cc_final: 0.7328 (mtpt) REVERT: P 51 GLN cc_start: 0.3948 (OUTLIER) cc_final: 0.2819 (pp30) REVERT: P 207 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.5217 (pp) REVERT: P 213 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6250 (m-40) REVERT: R 153 TYR cc_start: 0.7356 (p90) cc_final: 0.7130 (p90) REVERT: S 21 LEU cc_start: 0.6623 (mt) cc_final: 0.6382 (mp) REVERT: S 70 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8313 (mm) REVERT: S 97 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8203 (mm110) REVERT: V 186 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5139 (mtt180) REVERT: W 24 MET cc_start: 0.5936 (mmt) cc_final: 0.5627 (mmt) REVERT: W 126 THR cc_start: 0.8592 (p) cc_final: 0.8170 (m) REVERT: W 139 GLU cc_start: 0.5309 (tt0) cc_final: 0.5107 (tt0) REVERT: X 134 ASP cc_start: 0.5616 (p0) cc_final: 0.5223 (p0) REVERT: X 170 MET cc_start: 0.7293 (tpt) cc_final: 0.7032 (tpt) REVERT: Y 14 LEU cc_start: 0.7678 (tp) cc_final: 0.7217 (tt) REVERT: a 15 ILE cc_start: 0.5396 (OUTLIER) cc_final: 0.5110 (pt) REVERT: a 28 ARG cc_start: 0.5748 (ptt180) cc_final: 0.5271 (ptm160) REVERT: a 72 LEU cc_start: 0.7829 (pp) cc_final: 0.7545 (pp) REVERT: a 74 MET cc_start: 0.6053 (mtt) cc_final: 0.5803 (mtp) REVERT: a 173 ARG cc_start: 0.4951 (tpp-160) cc_final: 0.4570 (mtp85) outliers start: 92 outliers final: 30 residues processed: 1930 average time/residue: 0.2766 time to fit residues: 844.8993 Evaluate side-chains 1439 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 1397 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 222 PRO Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 186 ARG Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain P residue 51 GLN Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 140 GLU Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain P residue 222 PRO Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 186 ARG Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain a residue 15 ILE Chi-restraints excluded: chain b residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.4980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 68 HIS A 90 GLN B 51 GLN B 62 HIS B 87 HIS ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS C 166 ASN D 54 GLN E 155 HIS E 224 GLN F 43 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN H 110 GLN H 154 GLN ** I 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS L 162 GLN N 108 ASN N 147 GLN O 33 ASN O 68 HIS O 90 GLN P 51 GLN P 62 HIS P 87 HIS ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 69 ASN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 142 HIS Q 166 ASN R 54 GLN S 155 HIS S 224 GLN T 43 HIS ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN V 110 GLN V 154 GLN ** W 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 187 HIS ** Y 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN b 108 ASN b 147 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.198560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.192250 restraints weight = 72786.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.193921 restraints weight = 43408.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.194804 restraints weight = 29439.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.195292 restraints weight = 21360.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196093 restraints weight = 16536.148| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 44190 Z= 0.166 Angle : 0.784 16.320 59626 Z= 0.409 Chirality : 0.048 0.268 6732 Planarity : 0.007 0.172 7614 Dihedral : 10.401 149.199 6326 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.87 % Favored : 97.04 % Rotamer: Outliers : 4.31 % Allowed : 16.05 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -2.13 (0.10), residues: 5432 helix: -0.74 (0.10), residues: 1926 sheet: -2.12 (0.13), residues: 1278 loop : -1.38 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.001 ARG N 186 TYR 0.027 0.002 TYR Z 88 PHE 0.031 0.002 PHE X 116 TRP 0.019 0.002 TRP N 91 HIS 0.010 0.002 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00363 (44174) covalent geometry : angle 0.78373 (59622) SS BOND : bond 0.00390 ( 2) SS BOND : angle 1.77074 ( 4) hydrogen bonds : bond 0.04763 ( 1202) hydrogen bonds : angle 5.05213 ( 3606) Misc. bond : bond 0.00498 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1781 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1582 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR J 196 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR X 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 18 LEU cc_start: 0.7836 (mt) cc_final: 0.7635 (mt) REVERT: B 83 ARG cc_start: 0.6588 (mtt90) cc_final: 0.6339 (ttm110) REVERT: B 94 GLN cc_start: 0.6924 (mm110) cc_final: 0.6693 (mm-40) REVERT: B 96 TYR cc_start: 0.7075 (t80) cc_final: 0.6515 (t80) REVERT: B 139 ASN cc_start: 0.4151 (m-40) cc_final: 0.3740 (m-40) REVERT: C 119 GLN cc_start: 0.6267 (tp-100) cc_final: 0.6037 (tp-100) REVERT: D 94 HIS cc_start: 0.8055 (t-90) cc_final: 0.7713 (t-90) REVERT: D 153 TYR cc_start: 0.7537 (p90) cc_final: 0.7245 (p90) REVERT: D 233 GLU cc_start: 0.5279 (mt-10) cc_final: 0.4681 (mm-30) REVERT: E 86 LYS cc_start: 0.7189 (ttpt) cc_final: 0.6812 (mtpt) REVERT: F 18 ARG cc_start: 0.5138 (mpp-170) cc_final: 0.4893 (mpp-170) REVERT: F 180 MET cc_start: 0.4749 (mmm) cc_final: 0.3793 (mtm) REVERT: G 32 ASN cc_start: 0.6117 (m110) cc_final: 0.5764 (m-40) REVERT: G 167 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.6091 (pttt) REVERT: H 92 GLU cc_start: 0.6205 (pm20) cc_final: 0.5845 (pm20) REVERT: H 122 ARG cc_start: 0.7317 (ttt180) cc_final: 0.6746 (tmt170) REVERT: H 142 THR cc_start: 0.7087 (m) cc_final: 0.5613 (p) REVERT: J 93 LEU cc_start: 0.7985 (tp) cc_final: 0.7714 (tt) REVERT: K 14 LEU cc_start: 0.7290 (tp) cc_final: 0.7078 (tt) REVERT: L 143 TYR cc_start: 0.6547 (t80) cc_final: 0.5921 (t80) REVERT: M 28 ARG cc_start: 0.5760 (ptt180) cc_final: 0.4906 (ptm160) REVERT: M 72 LEU cc_start: 0.8265 (pp) cc_final: 0.8008 (pp) REVERT: P 18 LEU cc_start: 0.7832 (mt) cc_final: 0.7623 (mt) REVERT: P 94 GLN cc_start: 0.6851 (mm110) cc_final: 0.6606 (mm-40) REVERT: P 96 TYR cc_start: 0.7071 (t80) cc_final: 0.6531 (t80) REVERT: P 139 ASN cc_start: 0.4148 (m-40) cc_final: 0.3730 (m-40) REVERT: Q 119 GLN cc_start: 0.6259 (tp-100) cc_final: 0.6026 (tp-100) REVERT: R 94 HIS cc_start: 0.8049 (t-90) cc_final: 0.7703 (t-90) REVERT: R 153 TYR cc_start: 0.7536 (p90) cc_final: 0.7245 (p90) REVERT: R 233 GLU cc_start: 0.5315 (mt-10) cc_final: 0.4749 (mm-30) REVERT: S 86 LYS cc_start: 0.7180 (ttpt) cc_final: 0.6810 (mtpt) REVERT: T 16 GLN cc_start: 0.5271 (OUTLIER) cc_final: 0.4402 (mp10) REVERT: T 132 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7978 (mp) REVERT: T 180 MET cc_start: 0.4810 (mmm) cc_final: 0.3756 (mtm) REVERT: U 167 LYS cc_start: 0.6349 (OUTLIER) cc_final: 0.6103 (pttt) REVERT: V 92 GLU cc_start: 0.6237 (pm20) cc_final: 0.5866 (pm20) REVERT: V 142 THR cc_start: 0.6999 (m) cc_final: 0.5543 (p) REVERT: X 93 LEU cc_start: 0.7984 (tp) cc_final: 0.7705 (tt) REVERT: Y 14 LEU cc_start: 0.7281 (tp) cc_final: 0.7020 (tt) REVERT: Z 143 TYR cc_start: 0.6537 (t80) cc_final: 0.5927 (t80) REVERT: a 72 LEU cc_start: 0.8263 (pp) cc_final: 0.7985 (pp) REVERT: a 173 ARG cc_start: 0.5361 (tpp-160) cc_final: 0.4609 (mtp180) outliers start: 199 outliers final: 107 residues processed: 1699 average time/residue: 0.2764 time to fit residues: 750.3801 Evaluate side-chains 1446 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1335 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 141 ARG Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 147 GLN Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 227 HIS Chi-restraints excluded: chain T residue 16 GLN Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 141 ARG Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 147 GLN Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 240 optimal weight: 0.6980 chunk 443 optimal weight: 9.9990 chunk 531 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 chunk 344 optimal weight: 3.9990 chunk 347 optimal weight: 7.9990 chunk 534 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 452 optimal weight: 0.0470 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 168 ASN E 178 GLN F 20 HIS G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN I 85 GLN L 162 GLN M 131 GLN N 104 ASN O 33 ASN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 GLN P 168 ASN S 178 GLN T 20 HIS U 22 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN W 85 GLN ** Y 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN a 131 GLN b 104 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.194237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.187991 restraints weight = 73127.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.189569 restraints weight = 44589.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.190625 restraints weight = 29627.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.191405 restraints weight = 20862.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.191923 restraints weight = 15247.961| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44190 Z= 0.152 Angle : 0.695 15.567 59626 Z= 0.363 Chirality : 0.045 0.209 6732 Planarity : 0.006 0.208 7614 Dihedral : 9.698 141.406 6264 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 5.18 % Allowed : 19.02 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.81 (0.11), residues: 5432 helix: -0.34 (0.11), residues: 1946 sheet: -1.97 (0.13), residues: 1242 loop : -1.33 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG N 186 TYR 0.026 0.002 TYR Z 136 PHE 0.030 0.002 PHE F 97 TRP 0.015 0.001 TRP X 153 HIS 0.009 0.001 HIS V 66 Details of bonding type rmsd covalent geometry : bond 0.00340 (44174) covalent geometry : angle 0.69507 (59622) SS BOND : bond 0.00366 ( 2) SS BOND : angle 1.81460 ( 4) hydrogen bonds : bond 0.04446 ( 1202) hydrogen bonds : angle 4.75451 ( 3606) Misc. bond : bond 0.00511 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1678 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 1439 time to evaluate : 1.546 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 76 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6661 (mp) REVERT: B 96 TYR cc_start: 0.6735 (t80) cc_final: 0.6361 (t80) REVERT: B 217 PHE cc_start: 0.5345 (t80) cc_final: 0.5098 (t80) REVERT: C 12 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: C 119 GLN cc_start: 0.6276 (tp-100) cc_final: 0.5949 (tp-100) REVERT: D 94 HIS cc_start: 0.8012 (t-90) cc_final: 0.7642 (t-90) REVERT: D 153 TYR cc_start: 0.7480 (p90) cc_final: 0.7256 (p90) REVERT: D 212 ARG cc_start: 0.5873 (mmm-85) cc_final: 0.5622 (mmm-85) REVERT: E 86 LYS cc_start: 0.7215 (ttpt) cc_final: 0.6776 (mtpt) REVERT: F 18 ARG cc_start: 0.4933 (mpp-170) cc_final: 0.4553 (mpp-170) REVERT: F 77 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5837 (pp) REVERT: F 180 MET cc_start: 0.4938 (mmm) cc_final: 0.3623 (mtm) REVERT: G 22 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7779 (tp40) REVERT: G 167 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.6021 (pttt) REVERT: I 186 LEU cc_start: 0.4744 (OUTLIER) cc_final: 0.3747 (mt) REVERT: J 93 LEU cc_start: 0.7581 (tp) cc_final: 0.7348 (tt) REVERT: K 115 LEU cc_start: 0.6937 (pt) cc_final: 0.6642 (pp) REVERT: L 74 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6855 (tt) REVERT: L 143 TYR cc_start: 0.6717 (t80) cc_final: 0.6211 (t80) REVERT: M 22 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7784 (mm) REVERT: M 28 ARG cc_start: 0.5643 (ptt180) cc_final: 0.4899 (ptm160) REVERT: M 148 LEU cc_start: 0.5107 (tt) cc_final: 0.4365 (tp) REVERT: M 168 LEU cc_start: 0.5276 (mp) cc_final: 0.4885 (tp) REVERT: N 38 ASN cc_start: 0.5954 (t0) cc_final: 0.5553 (t0) REVERT: O 76 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6699 (mp) REVERT: P 96 TYR cc_start: 0.6713 (t80) cc_final: 0.6313 (t80) REVERT: P 217 PHE cc_start: 0.5344 (t80) cc_final: 0.5100 (t80) REVERT: Q 12 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: Q 119 GLN cc_start: 0.6269 (tp-100) cc_final: 0.5946 (tp-100) REVERT: R 94 HIS cc_start: 0.8021 (t-90) cc_final: 0.7643 (t-90) REVERT: R 153 TYR cc_start: 0.7485 (p90) cc_final: 0.7272 (p90) REVERT: R 212 ARG cc_start: 0.5879 (mmm-85) cc_final: 0.5626 (mmm-85) REVERT: S 86 LYS cc_start: 0.7208 (ttpt) cc_final: 0.6780 (mtpt) REVERT: T 6 TYR cc_start: 0.4015 (t80) cc_final: 0.3764 (t80) REVERT: T 16 GLN cc_start: 0.5105 (OUTLIER) cc_final: 0.4490 (mp10) REVERT: T 77 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5877 (pp) REVERT: T 180 MET cc_start: 0.5004 (mmm) cc_final: 0.3679 (mtm) REVERT: U 22 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7818 (tp40) REVERT: U 167 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.6059 (pttt) REVERT: X 93 LEU cc_start: 0.7587 (tp) cc_final: 0.7355 (tt) REVERT: Z 74 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6839 (tt) REVERT: Z 143 TYR cc_start: 0.6728 (t80) cc_final: 0.6255 (t80) REVERT: a 22 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7779 (mm) REVERT: a 91 MET cc_start: 0.6760 (ppp) cc_final: 0.6508 (ptm) REVERT: a 148 LEU cc_start: 0.5149 (tt) cc_final: 0.4384 (tp) REVERT: a 168 LEU cc_start: 0.5317 (mp) cc_final: 0.4923 (tp) REVERT: a 173 ARG cc_start: 0.5332 (tpp-160) cc_final: 0.4605 (mtp180) REVERT: b 38 ASN cc_start: 0.5956 (t0) cc_final: 0.5549 (t0) outliers start: 239 outliers final: 138 residues processed: 1576 average time/residue: 0.2523 time to fit residues: 637.3419 Evaluate side-chains 1470 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1316 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain T residue 16 GLN Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 8 PHE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 444 optimal weight: 0.0670 chunk 402 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 515 optimal weight: 8.9990 chunk 139 optimal weight: 0.0570 chunk 528 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 352 optimal weight: 10.0000 chunk 538 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN K 65 GLN N 104 ASN O 75 ASN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 HIS ** R 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN W 85 GLN ** Y 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 65 GLN b 104 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.196989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.190933 restraints weight = 72815.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.192458 restraints weight = 44265.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.193507 restraints weight = 29450.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.194265 restraints weight = 20549.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.194759 restraints weight = 15109.968| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44190 Z= 0.126 Angle : 0.651 15.855 59626 Z= 0.336 Chirality : 0.044 0.194 6732 Planarity : 0.005 0.093 7614 Dihedral : 9.208 138.957 6264 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 4.77 % Allowed : 20.73 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.51 (0.11), residues: 5432 helix: -0.05 (0.11), residues: 1954 sheet: -1.81 (0.14), residues: 1230 loop : -1.21 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG b 186 TYR 0.021 0.001 TYR Z 136 PHE 0.024 0.002 PHE F 97 TRP 0.019 0.001 TRP Z 55 HIS 0.019 0.001 HIS T 20 Details of bonding type rmsd covalent geometry : bond 0.00274 (44174) covalent geometry : angle 0.65099 (59622) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.29372 ( 4) hydrogen bonds : bond 0.04012 ( 1202) hydrogen bonds : angle 4.46472 ( 3606) Misc. bond : bond 0.00374 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1412 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 229 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6453 (mp) REVERT: B 96 TYR cc_start: 0.6688 (t80) cc_final: 0.6362 (t80) REVERT: B 102 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6390 (pm20) REVERT: C 12 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: C 119 GLN cc_start: 0.6257 (tp-100) cc_final: 0.5914 (tp-100) REVERT: D 153 TYR cc_start: 0.7607 (p90) cc_final: 0.7363 (p90) REVERT: E 86 LYS cc_start: 0.7224 (ttpt) cc_final: 0.6914 (mtpt) REVERT: E 97 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8370 (mm-40) REVERT: F 6 TYR cc_start: 0.4011 (t80) cc_final: 0.3802 (t80) REVERT: F 18 ARG cc_start: 0.5088 (mpp-170) cc_final: 0.4570 (mpp-170) REVERT: F 87 PHE cc_start: 0.7068 (t80) cc_final: 0.6653 (t80) REVERT: J 145 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.6181 (mtt) REVERT: J 182 MET cc_start: 0.4580 (mmt) cc_final: 0.4020 (mtp) REVERT: K 121 LEU cc_start: 0.6424 (mt) cc_final: 0.6026 (mt) REVERT: K 132 HIS cc_start: 0.5620 (m-70) cc_final: 0.5299 (m-70) REVERT: L 55 TRP cc_start: 0.7081 (m100) cc_final: 0.6830 (m100) REVERT: L 74 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6761 (tt) REVERT: L 89 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: L 143 TYR cc_start: 0.6422 (t80) cc_final: 0.6035 (t80) REVERT: M 22 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7696 (mm) REVERT: M 28 ARG cc_start: 0.5664 (ptt180) cc_final: 0.4836 (ptm160) REVERT: M 148 LEU cc_start: 0.4972 (tt) cc_final: 0.4400 (tp) REVERT: N 38 ASN cc_start: 0.5795 (t0) cc_final: 0.5338 (t0) REVERT: O 229 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.6411 (mp) REVERT: P 96 TYR cc_start: 0.6637 (t80) cc_final: 0.6346 (t80) REVERT: P 102 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6403 (pm20) REVERT: Q 12 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: Q 119 GLN cc_start: 0.6246 (tp-100) cc_final: 0.5903 (tp-100) REVERT: R 153 TYR cc_start: 0.7611 (p90) cc_final: 0.7379 (p90) REVERT: S 86 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6921 (mtpt) REVERT: S 97 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8361 (mm-40) REVERT: T 6 TYR cc_start: 0.3890 (t80) cc_final: 0.3688 (t80) REVERT: T 87 PHE cc_start: 0.7100 (t80) cc_final: 0.6671 (t80) REVERT: V 112 TYR cc_start: 0.6122 (m-80) cc_final: 0.5873 (m-80) REVERT: W 186 LEU cc_start: 0.4575 (OUTLIER) cc_final: 0.4229 (mt) REVERT: X 145 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6196 (mtt) REVERT: Y 121 LEU cc_start: 0.6404 (mt) cc_final: 0.6034 (mt) REVERT: Y 132 HIS cc_start: 0.5671 (m-70) cc_final: 0.5323 (m-70) REVERT: Z 74 ILE cc_start: 0.7146 (tt) cc_final: 0.6784 (tt) REVERT: Z 89 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: Z 143 TYR cc_start: 0.6487 (t80) cc_final: 0.6096 (t80) REVERT: a 22 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7706 (mm) REVERT: a 28 ARG cc_start: 0.5670 (ptt180) cc_final: 0.4868 (ptm160) REVERT: a 71 ARG cc_start: 0.6967 (tpp80) cc_final: 0.6452 (mmm-85) REVERT: a 148 LEU cc_start: 0.4946 (tt) cc_final: 0.4299 (tp) REVERT: a 173 ARG cc_start: 0.5368 (tpp-160) cc_final: 0.4602 (mtp180) REVERT: b 38 ASN cc_start: 0.5783 (t0) cc_final: 0.5372 (t0) REVERT: b 112 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.5965 (mp) outliers start: 220 outliers final: 122 residues processed: 1546 average time/residue: 0.2505 time to fit residues: 623.1450 Evaluate side-chains 1444 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1307 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 26 ARG Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 212 GLU Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 26 ARG Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 171 optimal weight: 2.9990 chunk 459 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 262 optimal weight: 0.9990 chunk 441 optimal weight: 8.9990 chunk 397 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 440 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 450 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS E 224 GLN E 225 ASN F 69 HIS G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 62 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 ASN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 GLN S 225 ASN T 20 HIS T 69 HIS U 22 GLN V 7 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN V 62 GLN ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 6 ASN ** Y 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.198700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.193501 restraints weight = 74796.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.194890 restraints weight = 45699.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195806 restraints weight = 29943.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.196457 restraints weight = 20847.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.196864 restraints weight = 15114.885| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44190 Z= 0.160 Angle : 0.680 15.939 59626 Z= 0.351 Chirality : 0.045 0.234 6732 Planarity : 0.006 0.242 7614 Dihedral : 9.152 137.079 6264 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 5.83 % Allowed : 21.38 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.54 (0.11), residues: 5432 helix: -0.08 (0.11), residues: 1956 sheet: -1.96 (0.14), residues: 1224 loop : -1.12 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG N 186 TYR 0.021 0.002 TYR Z 88 PHE 0.035 0.002 PHE Z 54 TRP 0.017 0.002 TRP X 153 HIS 0.011 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00360 (44174) covalent geometry : angle 0.67978 (59622) SS BOND : bond 0.00315 ( 2) SS BOND : angle 1.40499 ( 4) hydrogen bonds : bond 0.04125 ( 1202) hydrogen bonds : angle 4.44975 ( 3606) Misc. bond : bond 0.00517 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1599 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 1330 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 96 TYR cc_start: 0.6550 (t80) cc_final: 0.6293 (t80) REVERT: B 217 PHE cc_start: 0.5103 (t80) cc_final: 0.4826 (t80) REVERT: C 6 ASP cc_start: 0.5666 (t0) cc_final: 0.5241 (t0) REVERT: C 12 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: C 119 GLN cc_start: 0.6098 (tp-100) cc_final: 0.5707 (tp-100) REVERT: D 124 ARG cc_start: 0.6551 (mtm-85) cc_final: 0.6305 (mtm180) REVERT: D 153 TYR cc_start: 0.7605 (p90) cc_final: 0.7349 (p90) REVERT: E 86 LYS cc_start: 0.7271 (ttpt) cc_final: 0.6845 (mtpt) REVERT: E 91 LYS cc_start: 0.7568 (tmtt) cc_final: 0.7317 (tttm) REVERT: E 97 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8377 (mm-40) REVERT: F 18 ARG cc_start: 0.5044 (mpp-170) cc_final: 0.4835 (mpt90) REVERT: G 167 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6238 (pttt) REVERT: I 186 LEU cc_start: 0.4875 (OUTLIER) cc_final: 0.3922 (mt) REVERT: L 74 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6858 (tt) REVERT: L 89 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: L 100 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6542 (mtm) REVERT: M 22 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7667 (mm) REVERT: M 28 ARG cc_start: 0.5742 (ptt180) cc_final: 0.5000 (ptm160) REVERT: N 27 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7646 (mp) REVERT: N 76 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5870 (pp) REVERT: N 112 ILE cc_start: 0.6239 (OUTLIER) cc_final: 0.5894 (mp) REVERT: N 124 TYR cc_start: 0.7055 (t80) cc_final: 0.6779 (t80) REVERT: N 132 TYR cc_start: 0.5979 (p90) cc_final: 0.5749 (p90) REVERT: P 96 TYR cc_start: 0.6565 (t80) cc_final: 0.6339 (t80) REVERT: P 217 PHE cc_start: 0.5101 (t80) cc_final: 0.4822 (t80) REVERT: Q 6 ASP cc_start: 0.5652 (t0) cc_final: 0.5244 (t0) REVERT: Q 12 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: Q 119 GLN cc_start: 0.6091 (tp-100) cc_final: 0.5681 (tp-100) REVERT: R 124 ARG cc_start: 0.6561 (mtm-85) cc_final: 0.6309 (mtm180) REVERT: S 86 LYS cc_start: 0.7230 (ttpt) cc_final: 0.6820 (mtpt) REVERT: S 91 LYS cc_start: 0.7563 (tmtt) cc_final: 0.7326 (tttm) REVERT: S 97 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8382 (mm-40) REVERT: T 6 TYR cc_start: 0.4130 (t80) cc_final: 0.3823 (t80) REVERT: V 153 LEU cc_start: 0.6942 (pp) cc_final: 0.6721 (pp) REVERT: W 186 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.4614 (mt) REVERT: X 82 LYS cc_start: 0.4374 (tppt) cc_final: 0.4156 (mtpp) REVERT: Y 132 HIS cc_start: 0.5770 (m-70) cc_final: 0.5358 (m-70) REVERT: Z 74 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6806 (tt) REVERT: Z 89 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: Z 143 TYR cc_start: 0.6809 (t80) cc_final: 0.6452 (t80) REVERT: a 22 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7675 (mm) REVERT: a 28 ARG cc_start: 0.5668 (ptt180) cc_final: 0.4961 (ptm160) REVERT: a 173 ARG cc_start: 0.5133 (tpp-160) cc_final: 0.4455 (mtp180) REVERT: b 76 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5865 (pp) REVERT: b 112 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5825 (mp) outliers start: 269 outliers final: 184 residues processed: 1487 average time/residue: 0.2451 time to fit residues: 588.7523 Evaluate side-chains 1468 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 1267 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 149 CYS Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 192 optimal weight: 10.0000 chunk 447 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 318 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 499 optimal weight: 9.9990 chunk 505 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 90 GLN G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 62 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 ASN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 ASN Q 102 GLN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN S 155 HIS S 225 ASN ** T 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS b 104 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.190642 restraints weight = 71776.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.192002 restraints weight = 44491.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.192891 restraints weight = 29542.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.193507 restraints weight = 20935.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.193936 restraints weight = 15611.909| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 44190 Z= 0.167 Angle : 0.688 16.000 59626 Z= 0.354 Chirality : 0.046 0.258 6732 Planarity : 0.006 0.136 7614 Dihedral : 9.093 136.669 6264 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 6.18 % Allowed : 22.72 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.53 (0.11), residues: 5432 helix: -0.07 (0.11), residues: 1966 sheet: -1.94 (0.14), residues: 1238 loop : -1.14 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 186 TYR 0.032 0.002 TYR V 90 PHE 0.028 0.002 PHE F 97 TRP 0.019 0.002 TRP X 153 HIS 0.027 0.001 HIS T 20 Details of bonding type rmsd covalent geometry : bond 0.00381 (44174) covalent geometry : angle 0.68777 (59622) SS BOND : bond 0.00216 ( 2) SS BOND : angle 1.20258 ( 4) hydrogen bonds : bond 0.04145 ( 1202) hydrogen bonds : angle 4.41669 ( 3606) Misc. bond : bond 0.00351 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1577 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 285 poor density : 1292 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6506 (mp) REVERT: B 96 TYR cc_start: 0.6597 (t80) cc_final: 0.6144 (t80) REVERT: C 6 ASP cc_start: 0.5547 (t0) cc_final: 0.5082 (t0) REVERT: C 12 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: C 119 GLN cc_start: 0.6122 (tp-100) cc_final: 0.5664 (tp-100) REVERT: D 153 TYR cc_start: 0.7694 (p90) cc_final: 0.7399 (p90) REVERT: E 86 LYS cc_start: 0.7424 (ttpt) cc_final: 0.6893 (mtpt) REVERT: E 91 LYS cc_start: 0.7757 (tmtt) cc_final: 0.7491 (tttm) REVERT: E 189 MET cc_start: 0.3443 (OUTLIER) cc_final: 0.2497 (tpp) REVERT: G 167 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6267 (pttt) REVERT: I 186 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4670 (mt) REVERT: I 203 ARG cc_start: 0.5258 (mmt90) cc_final: 0.4347 (ptm-80) REVERT: L 56 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6439 (mt-10) REVERT: L 74 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6976 (tt) REVERT: L 89 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6925 (tm-30) REVERT: M 28 ARG cc_start: 0.5890 (ptt180) cc_final: 0.5066 (ptm160) REVERT: N 76 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5981 (pp) REVERT: N 112 ILE cc_start: 0.6247 (OUTLIER) cc_final: 0.5952 (mp) REVERT: N 124 TYR cc_start: 0.7051 (t80) cc_final: 0.6772 (t80) REVERT: N 186 ARG cc_start: 0.4741 (OUTLIER) cc_final: 0.2098 (tpm170) REVERT: O 76 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6572 (mp) REVERT: O 229 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6512 (mp) REVERT: P 96 TYR cc_start: 0.6642 (t80) cc_final: 0.6178 (t80) REVERT: Q 6 ASP cc_start: 0.5536 (t0) cc_final: 0.5073 (t0) REVERT: Q 12 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7234 (m-80) REVERT: S 91 LYS cc_start: 0.7764 (tmtt) cc_final: 0.7501 (tttm) REVERT: U 167 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6230 (pttt) REVERT: W 81 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5768 (ttt-90) REVERT: W 186 LEU cc_start: 0.4912 (OUTLIER) cc_final: 0.4650 (mt) REVERT: W 203 ARG cc_start: 0.5277 (mmt90) cc_final: 0.4383 (ptm-80) REVERT: X 82 LYS cc_start: 0.4449 (tppt) cc_final: 0.3958 (mtpp) REVERT: Z 56 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6441 (mt-10) REVERT: Z 74 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7007 (tt) REVERT: Z 89 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: a 28 ARG cc_start: 0.5869 (ptt180) cc_final: 0.5091 (ptm160) REVERT: a 148 LEU cc_start: 0.5127 (tt) cc_final: 0.4188 (tp) REVERT: a 173 ARG cc_start: 0.5353 (tpp-160) cc_final: 0.4759 (mtp85) REVERT: b 5 MET cc_start: 0.6060 (mmt) cc_final: 0.5752 (mmt) REVERT: b 76 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5960 (pp) REVERT: b 112 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5977 (mp) REVERT: b 186 ARG cc_start: 0.4855 (OUTLIER) cc_final: 0.2241 (tpm170) outliers start: 285 outliers final: 192 residues processed: 1459 average time/residue: 0.2435 time to fit residues: 574.6561 Evaluate side-chains 1452 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 1239 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 98 ASN Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 104 ASN Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 122 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 481 optimal weight: 0.9990 chunk 459 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 480 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 420 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 225 ASN F 117 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 ASN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN T 90 GLN T 117 GLN U 22 GLN V 7 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 55 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.192611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.187400 restraints weight = 71969.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.188701 restraints weight = 44223.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.189630 restraints weight = 29589.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.190243 restraints weight = 20869.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.190661 restraints weight = 15502.407| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 44190 Z= 0.211 Angle : 0.751 16.221 59626 Z= 0.387 Chirality : 0.048 0.258 6732 Planarity : 0.006 0.148 7614 Dihedral : 9.269 136.193 6262 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 6.35 % Allowed : 23.20 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.77 (0.11), residues: 5432 helix: -0.25 (0.11), residues: 1952 sheet: -2.08 (0.13), residues: 1296 loop : -1.25 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG b 186 TYR 0.029 0.002 TYR H 61 PHE 0.027 0.002 PHE F 97 TRP 0.026 0.002 TRP J 153 HIS 0.009 0.002 HIS V 66 Details of bonding type rmsd covalent geometry : bond 0.00482 (44174) covalent geometry : angle 0.75046 (59622) SS BOND : bond 0.00233 ( 2) SS BOND : angle 1.62028 ( 4) hydrogen bonds : bond 0.04447 ( 1202) hydrogen bonds : angle 4.61637 ( 3606) Misc. bond : bond 0.00365 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1577 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 293 poor density : 1284 time to evaluate : 1.553 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 229 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6481 (mp) REVERT: C 12 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: C 25 MET cc_start: 0.6496 (mmp) cc_final: 0.6227 (mmp) REVERT: D 153 TYR cc_start: 0.7751 (p90) cc_final: 0.7461 (p90) REVERT: E 86 LYS cc_start: 0.7560 (ttpt) cc_final: 0.7015 (mtpt) REVERT: E 91 LYS cc_start: 0.7831 (tmtt) cc_final: 0.7580 (tttm) REVERT: E 189 MET cc_start: 0.3504 (OUTLIER) cc_final: 0.2576 (tpp) REVERT: G 167 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6306 (pttt) REVERT: I 186 LEU cc_start: 0.5101 (OUTLIER) cc_final: 0.4854 (mt) REVERT: I 203 ARG cc_start: 0.5231 (mmt90) cc_final: 0.4305 (ptm-80) REVERT: J 93 LEU cc_start: 0.7873 (tp) cc_final: 0.7599 (tt) REVERT: K 41 LYS cc_start: 0.5913 (mptt) cc_final: 0.5464 (mptt) REVERT: L 56 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6554 (mt-10) REVERT: L 74 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7130 (tt) REVERT: M 28 ARG cc_start: 0.6021 (ptt180) cc_final: 0.5177 (ptm160) REVERT: M 66 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8201 (mtmm) REVERT: N 76 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6004 (pp) REVERT: N 186 ARG cc_start: 0.4367 (OUTLIER) cc_final: 0.1901 (tpm170) REVERT: O 229 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6506 (mp) REVERT: Q 12 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: Q 159 TRP cc_start: 0.6343 (m100) cc_final: 0.6123 (m100) REVERT: R 153 TYR cc_start: 0.7645 (p90) cc_final: 0.7415 (p90) REVERT: S 91 LYS cc_start: 0.7837 (tmtt) cc_final: 0.7589 (tttm) REVERT: S 189 MET cc_start: 0.3492 (OUTLIER) cc_final: 0.2504 (tpp) REVERT: S 224 GLN cc_start: 0.4792 (OUTLIER) cc_final: 0.4571 (pt0) REVERT: U 167 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6291 (pttt) REVERT: V 134 TYR cc_start: 0.7506 (m-80) cc_final: 0.7297 (m-80) REVERT: W 81 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5594 (ttt-90) REVERT: W 186 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4279 (mt) REVERT: W 203 ARG cc_start: 0.5271 (mmt90) cc_final: 0.4309 (ptm-80) REVERT: X 82 LYS cc_start: 0.4531 (tppt) cc_final: 0.4262 (mtpp) REVERT: X 93 LEU cc_start: 0.7933 (tp) cc_final: 0.7651 (tt) REVERT: Y 41 LYS cc_start: 0.5890 (mptt) cc_final: 0.5433 (mptt) REVERT: Z 56 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6576 (mt-10) REVERT: Z 74 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7158 (tt) REVERT: Z 89 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: a 28 ARG cc_start: 0.5975 (ptt180) cc_final: 0.5099 (ptm160) REVERT: a 66 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8090 (mtmm) REVERT: a 173 ARG cc_start: 0.5477 (tpp-160) cc_final: 0.4802 (mtp85) REVERT: b 5 MET cc_start: 0.6100 (mmt) cc_final: 0.5779 (mmt) REVERT: b 76 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5942 (pp) REVERT: b 112 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.6092 (mp) REVERT: b 186 ARG cc_start: 0.4339 (OUTLIER) cc_final: 0.1741 (tpm170) outliers start: 293 outliers final: 205 residues processed: 1450 average time/residue: 0.2438 time to fit residues: 572.8585 Evaluate side-chains 1450 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 1225 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 224 GLN Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 122 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 275 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 430 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN G 22 GLN G 32 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN J 6 ASN ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 82 ASN M 77 HIS M 80 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS a 80 ASN b 104 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.189722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.184250 restraints weight = 73196.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.185613 restraints weight = 45761.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.186591 restraints weight = 30539.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187242 restraints weight = 21548.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.187698 restraints weight = 15983.482| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 44190 Z= 0.265 Angle : 0.825 16.355 59626 Z= 0.427 Chirality : 0.051 0.250 6732 Planarity : 0.007 0.156 7614 Dihedral : 9.585 135.011 6262 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.87 % Favored : 94.00 % Rotamer: Outliers : 6.33 % Allowed : 23.81 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -2.13 (0.11), residues: 5432 helix: -0.57 (0.11), residues: 1950 sheet: -2.25 (0.13), residues: 1256 loop : -1.48 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 186 TYR 0.035 0.003 TYR H 61 PHE 0.037 0.003 PHE T 97 TRP 0.031 0.003 TRP X 153 HIS 0.013 0.002 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00606 (44174) covalent geometry : angle 0.82438 (59622) SS BOND : bond 0.00137 ( 2) SS BOND : angle 1.93574 ( 4) hydrogen bonds : bond 0.04880 ( 1202) hydrogen bonds : angle 4.92662 ( 3606) Misc. bond : bond 0.00402 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 1276 time to evaluate : 1.666 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 229 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6533 (mp) REVERT: C 12 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: C 25 MET cc_start: 0.6572 (mmp) cc_final: 0.6330 (mmp) REVERT: D 95 ARG cc_start: 0.6427 (mmm160) cc_final: 0.6122 (tpt90) REVERT: D 153 TYR cc_start: 0.7745 (p90) cc_final: 0.7492 (p90) REVERT: E 86 LYS cc_start: 0.7559 (ttpt) cc_final: 0.7054 (mtpt) REVERT: E 91 LYS cc_start: 0.7792 (tmtt) cc_final: 0.7545 (tttm) REVERT: E 189 MET cc_start: 0.3644 (OUTLIER) cc_final: 0.2824 (tpp) REVERT: F 125 ARG cc_start: 0.5875 (mmt180) cc_final: 0.5417 (mmt90) REVERT: G 167 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6403 (pptt) REVERT: I 81 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5778 (ttt-90) REVERT: I 186 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4034 (mt) REVERT: J 6 ASN cc_start: 0.6258 (OUTLIER) cc_final: 0.5979 (t0) REVERT: J 26 ARG cc_start: 0.7008 (tmt-80) cc_final: 0.6667 (tmt-80) REVERT: K 41 LYS cc_start: 0.5940 (mptt) cc_final: 0.5656 (mptt) REVERT: K 85 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7442 (ttp80) REVERT: L 56 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6582 (mt-10) REVERT: L 143 TYR cc_start: 0.7371 (t80) cc_final: 0.4671 (t80) REVERT: M 28 ARG cc_start: 0.6074 (ptt180) cc_final: 0.5030 (ptm160) REVERT: M 66 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8105 (mtmm) REVERT: N 76 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6158 (pp) REVERT: N 77 LEU cc_start: 0.7244 (mt) cc_final: 0.6927 (mt) REVERT: N 186 ARG cc_start: 0.4717 (OUTLIER) cc_final: 0.4235 (tpm170) REVERT: O 229 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6465 (mp) REVERT: P 96 TYR cc_start: 0.6723 (t80) cc_final: 0.6523 (t80) REVERT: Q 12 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: Q 25 MET cc_start: 0.6641 (mmp) cc_final: 0.6358 (mmp) REVERT: Q 48 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5804 (tp30) REVERT: Q 119 GLN cc_start: 0.6211 (tp-100) cc_final: 0.5990 (tp-100) REVERT: R 95 ARG cc_start: 0.6363 (mmm160) cc_final: 0.6100 (tpt90) REVERT: R 153 TYR cc_start: 0.7679 (p90) cc_final: 0.7273 (p90) REVERT: S 91 LYS cc_start: 0.7780 (tmtt) cc_final: 0.7551 (tttm) REVERT: S 189 MET cc_start: 0.3614 (OUTLIER) cc_final: 0.2784 (tpp) REVERT: T 125 ARG cc_start: 0.5891 (mmt180) cc_final: 0.5453 (mmt90) REVERT: U 167 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6378 (pttt) REVERT: V 19 ARG cc_start: 0.7264 (mtp180) cc_final: 0.6845 (mtp180) REVERT: W 81 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5691 (ttt-90) REVERT: W 186 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4031 (mt) REVERT: X 26 ARG cc_start: 0.7075 (tmt-80) cc_final: 0.6664 (tmt-80) REVERT: Z 56 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6541 (mt-10) REVERT: Z 143 TYR cc_start: 0.7437 (t80) cc_final: 0.4770 (t80) REVERT: a 28 ARG cc_start: 0.6079 (ptt180) cc_final: 0.5096 (ptm160) REVERT: a 173 ARG cc_start: 0.5593 (tpp-160) cc_final: 0.4948 (mtp85) REVERT: b 76 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6105 (pp) REVERT: b 77 LEU cc_start: 0.7238 (mt) cc_final: 0.6928 (mt) REVERT: b 112 ILE cc_start: 0.6179 (OUTLIER) cc_final: 0.5959 (mp) REVERT: b 186 ARG cc_start: 0.4689 (OUTLIER) cc_final: 0.4209 (tpm170) outliers start: 292 outliers final: 224 residues processed: 1462 average time/residue: 0.2602 time to fit residues: 614.0780 Evaluate side-chains 1477 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 1233 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 170 ILE Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 75 MET Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 45 MET Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 104 ASN Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 122 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 342 optimal weight: 9.9990 chunk 538 optimal weight: 0.5980 chunk 269 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 470 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 344 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 462 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN N 61 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN W 30 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 187 HIS ** Y 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 82 ASN a 77 HIS a 80 ASN b 61 GLN ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.194302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.189043 restraints weight = 71789.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.190327 restraints weight = 44166.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.191272 restraints weight = 29555.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.191910 restraints weight = 20772.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.192341 restraints weight = 15273.304| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 44190 Z= 0.158 Angle : 0.729 15.764 59626 Z= 0.374 Chirality : 0.047 0.339 6732 Planarity : 0.006 0.128 7614 Dihedral : 9.260 133.933 6262 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.23 % Favored : 95.64 % Rotamer: Outliers : 4.75 % Allowed : 26.08 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.86 (0.11), residues: 5432 helix: -0.30 (0.11), residues: 1956 sheet: -2.11 (0.13), residues: 1238 loop : -1.38 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 186 TYR 0.025 0.002 TYR B 96 PHE 0.033 0.002 PHE T 97 TRP 0.023 0.002 TRP J 153 HIS 0.016 0.001 HIS K 189 Details of bonding type rmsd covalent geometry : bond 0.00366 (44174) covalent geometry : angle 0.72856 (59622) SS BOND : bond 0.00066 ( 2) SS BOND : angle 1.79671 ( 4) hydrogen bonds : bond 0.04302 ( 1202) hydrogen bonds : angle 4.65336 ( 3606) Misc. bond : bond 0.00363 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 1275 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.5222 (OUTLIER) cc_final: 0.4751 (mm-30) REVERT: B 70 HIS cc_start: 0.5417 (OUTLIER) cc_final: 0.4647 (p90) REVERT: B 83 ARG cc_start: 0.6809 (mtt90) cc_final: 0.6545 (ttm110) REVERT: C 12 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: C 25 MET cc_start: 0.6427 (mmp) cc_final: 0.6226 (mmp) REVERT: C 119 GLN cc_start: 0.6071 (tp-100) cc_final: 0.5809 (tp-100) REVERT: D 153 TYR cc_start: 0.7673 (p90) cc_final: 0.7347 (p90) REVERT: D 184 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5753 (t70) REVERT: E 86 LYS cc_start: 0.7434 (ttpt) cc_final: 0.6857 (mtpt) REVERT: F 125 ARG cc_start: 0.5603 (mmt180) cc_final: 0.5328 (mmt90) REVERT: G 167 LYS cc_start: 0.6613 (OUTLIER) cc_final: 0.6377 (pptt) REVERT: H 147 MET cc_start: 0.5661 (mtt) cc_final: 0.5231 (ttm) REVERT: I 81 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5638 (ttt-90) REVERT: I 85 GLN cc_start: 0.6828 (mt0) cc_final: 0.6574 (mt0) REVERT: I 186 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4334 (mt) REVERT: J 26 ARG cc_start: 0.6781 (tmt-80) cc_final: 0.6274 (tmt-80) REVERT: J 93 LEU cc_start: 0.7749 (tp) cc_final: 0.7459 (tt) REVERT: K 85 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7291 (ttp80) REVERT: K 139 THR cc_start: 0.6326 (OUTLIER) cc_final: 0.6039 (m) REVERT: L 56 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6580 (mt-10) REVERT: L 74 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7054 (tt) REVERT: M 28 ARG cc_start: 0.5964 (ptt180) cc_final: 0.5108 (ptm160) REVERT: M 66 LYS cc_start: 0.8350 (mtmm) cc_final: 0.8013 (mtmm) REVERT: N 76 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6170 (pp) REVERT: N 186 ARG cc_start: 0.4386 (OUTLIER) cc_final: 0.1771 (tpm170) REVERT: O 76 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.6615 (mp) REVERT: P 70 HIS cc_start: 0.5365 (OUTLIER) cc_final: 0.4564 (p90) REVERT: P 83 ARG cc_start: 0.6799 (mtt90) cc_final: 0.6542 (ttm110) REVERT: Q 12 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: R 153 TYR cc_start: 0.7663 (p90) cc_final: 0.7238 (p90) REVERT: R 184 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5857 (t70) REVERT: T 125 ARG cc_start: 0.5701 (mmt180) cc_final: 0.5383 (mmt90) REVERT: U 167 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6257 (pptt) REVERT: W 81 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.5506 (ttt-90) REVERT: W 186 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4851 (mt) REVERT: X 26 ARG cc_start: 0.6765 (tmt-80) cc_final: 0.6299 (tmt-80) REVERT: X 93 LEU cc_start: 0.7675 (tp) cc_final: 0.7413 (tt) REVERT: Y 41 LYS cc_start: 0.5595 (mptt) cc_final: 0.5114 (mptt) REVERT: Z 74 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7101 (tt) REVERT: Z 143 TYR cc_start: 0.7102 (t80) cc_final: 0.4822 (t80) REVERT: a 28 ARG cc_start: 0.5987 (ptt180) cc_final: 0.5113 (ptm160) REVERT: a 173 ARG cc_start: 0.5624 (tpp-160) cc_final: 0.4781 (mtp85) REVERT: b 76 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6156 (pp) REVERT: b 112 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5752 (mp) REVERT: b 186 ARG cc_start: 0.4299 (OUTLIER) cc_final: 0.1692 (tpm170) outliers start: 219 outliers final: 164 residues processed: 1410 average time/residue: 0.2886 time to fit residues: 651.5274 Evaluate side-chains 1415 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 1228 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 170 ILE Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 45 MET Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 122 LEU Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 132 optimal weight: 0.0670 chunk 450 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 444 optimal weight: 0.3980 chunk 537 optimal weight: 3.9990 chunk 470 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 ASN K 24 ASN M 77 HIS ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 6 ASN Y 24 ASN ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN a 77 HIS ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.198344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.192911 restraints weight = 71360.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.194283 restraints weight = 43448.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.195257 restraints weight = 28813.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195900 restraints weight = 20120.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.196362 restraints weight = 15003.417| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44190 Z= 0.134 Angle : 0.708 15.476 59626 Z= 0.363 Chirality : 0.046 0.289 6732 Planarity : 0.006 0.119 7614 Dihedral : 8.896 129.813 6261 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 3.77 % Allowed : 27.71 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.57 (0.11), residues: 5432 helix: -0.04 (0.11), residues: 1956 sheet: -2.00 (0.14), residues: 1258 loop : -1.19 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG b 186 TYR 0.027 0.002 TYR Q 136 PHE 0.033 0.002 PHE F 97 TRP 0.037 0.002 TRP Q 159 HIS 0.015 0.001 HIS K 189 Details of bonding type rmsd covalent geometry : bond 0.00305 (44174) covalent geometry : angle 0.70771 (59622) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.49972 ( 4) hydrogen bonds : bond 0.04027 ( 1202) hydrogen bonds : angle 4.50503 ( 3606) Misc. bond : bond 0.00325 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 1304 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.5114 (OUTLIER) cc_final: 0.4660 (mm-30) REVERT: B 70 HIS cc_start: 0.5265 (OUTLIER) cc_final: 0.4631 (p90) REVERT: C 12 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: D 153 TYR cc_start: 0.7608 (p90) cc_final: 0.7334 (p90) REVERT: E 86 LYS cc_start: 0.7438 (ttpt) cc_final: 0.6830 (mtpt) REVERT: E 91 LYS cc_start: 0.7563 (tmtt) cc_final: 0.7220 (tttm) REVERT: F 125 ARG cc_start: 0.5482 (mmt180) cc_final: 0.5261 (mmt90) REVERT: F 180 MET cc_start: 0.5514 (tpp) cc_final: 0.4868 (mpp) REVERT: H 103 TRP cc_start: 0.5814 (OUTLIER) cc_final: 0.4787 (t60) REVERT: I 203 ARG cc_start: 0.4894 (mmt90) cc_final: 0.4022 (ptm-80) REVERT: J 26 ARG cc_start: 0.6622 (tmt-80) cc_final: 0.6074 (tmt-80) REVERT: L 56 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6544 (mt-10) REVERT: L 74 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6879 (tt) REVERT: L 140 ASP cc_start: 0.5886 (m-30) cc_final: 0.5278 (m-30) REVERT: M 28 ARG cc_start: 0.5920 (ptt180) cc_final: 0.5141 (ptm160) REVERT: M 66 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7992 (mtmm) REVERT: M 148 LEU cc_start: 0.5268 (tt) cc_final: 0.4425 (tp) REVERT: N 76 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5994 (pp) REVERT: N 186 ARG cc_start: 0.4601 (OUTLIER) cc_final: 0.1672 (tpm170) REVERT: O 76 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6512 (mp) REVERT: P 70 HIS cc_start: 0.5343 (OUTLIER) cc_final: 0.4676 (p90) REVERT: Q 12 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: R 153 TYR cc_start: 0.7505 (p90) cc_final: 0.7211 (p90) REVERT: S 91 LYS cc_start: 0.7613 (tmtt) cc_final: 0.7350 (tttm) REVERT: T 125 ARG cc_start: 0.5565 (mmt180) cc_final: 0.5348 (mmt90) REVERT: W 203 ARG cc_start: 0.4905 (mmt90) cc_final: 0.4025 (ptm-80) REVERT: X 26 ARG cc_start: 0.6608 (tmt-80) cc_final: 0.6026 (tmt-80) REVERT: Z 74 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.6948 (tt) REVERT: a 28 ARG cc_start: 0.6000 (ptt180) cc_final: 0.5226 (ptm160) REVERT: a 148 LEU cc_start: 0.4978 (tt) cc_final: 0.4164 (tp) REVERT: b 76 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5955 (pp) REVERT: b 112 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5676 (mp) REVERT: b 186 ARG cc_start: 0.4335 (OUTLIER) cc_final: 0.1592 (tpm170) outliers start: 174 outliers final: 136 residues processed: 1413 average time/residue: 0.2962 time to fit residues: 670.1395 Evaluate side-chains 1392 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1242 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 170 ILE Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 45 MET Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 11 optimal weight: 4.9990 chunk 450 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 454 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 287 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 478 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 225 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN J 6 ASN J 71 ASN J 172 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 ASN X 172 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 189 HIS a 77 HIS ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.198976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.193712 restraints weight = 71673.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.194965 restraints weight = 44848.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.195907 restraints weight = 30317.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.196520 restraints weight = 21549.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.196985 restraints weight = 15912.716| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 44190 Z= 0.141 Angle : 0.719 15.333 59626 Z= 0.368 Chirality : 0.046 0.286 6732 Planarity : 0.006 0.119 7614 Dihedral : 8.794 127.248 6261 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Rotamer: Outliers : 3.49 % Allowed : 28.12 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.47 (0.11), residues: 5432 helix: -0.01 (0.11), residues: 1952 sheet: -1.92 (0.14), residues: 1268 loop : -1.07 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG b 186 TYR 0.031 0.002 TYR Q 136 PHE 0.033 0.002 PHE T 97 TRP 0.037 0.002 TRP N 107 HIS 0.015 0.001 HIS K 189 Details of bonding type rmsd covalent geometry : bond 0.00323 (44174) covalent geometry : angle 0.71941 (59622) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.26351 ( 4) hydrogen bonds : bond 0.04058 ( 1202) hydrogen bonds : angle 4.48779 ( 3606) Misc. bond : bond 0.00309 ( 14) =============================================================================== Job complete usr+sys time: 10448.32 seconds wall clock time: 180 minutes 9.55 seconds (10809.55 seconds total)