Starting phenix.real_space_refine on Sun Mar 24 18:05:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/03_2024/5a0q_2981_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/03_2024/5a0q_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/03_2024/5a0q_2981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/03_2024/5a0q_2981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/03_2024/5a0q_2981_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a0q_2981/03_2024/5a0q_2981_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 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-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 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-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 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-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 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-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 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-6': 1, 'KNM:plan-4': 1, 'KNM:plan-5': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 21.30, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.83 Conformation dependent library (CDL) restraints added in 7.4 seconds 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... running ksdssp... Secondary structure from input PDB file: 142 helices and 62 sheets defined 34.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 84 through 104 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 205 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 121 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) Processing helix chain 'B' and resid 166 through 175 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 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' 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 81 through 101 removed outlier: 4.314A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) 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 117 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 185 through 197 removed outlier: 4.060A pdb=" N LEU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.591A pdb=" N LYS D 227 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL D 229 " --> pdb=" O GLU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 234 No H-bonds generated for 'chain 'D' and resid 231 through 234' 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 117 removed outlier: 3.775A pdb=" N VAL E 116 " --> pdb=" O VAL E 112 " (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 195 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 173 through 178 Processing helix chain 'G' and resid 181 through 183 No H-bonds generated for 'chain 'G' and resid 181 through 183' 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 139 removed outlier: 4.360A pdb=" N GLY H 137 " --> 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 131 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 152 through 165 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 95 Processing helix chain 'J' and resid 146 through 149 No H-bonds generated for 'chain 'J' and resid 146 through 149' 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 50 through 71 removed outlier: 3.612A pdb=" N THR K 53 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN K 55 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE K 56 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU K 58 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS K 62 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN K 65 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR K 67 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN K 71 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 92 Processing helix chain 'K' and resid 135 through 146 removed outlier: 3.696A pdb=" N THR K 139 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU K 140 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER K 141 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K 143 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP K 144 " --> pdb=" O SER K 141 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR K 146 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 169 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 69 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 164 Processing helix chain 'M' and resid 58 through 78 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 97 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 101 Processing helix chain 'N' and resid 146 through 154 removed outlier: 3.905A pdb=" N VAL N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 172 removed outlier: 3.729A pdb=" N ARG N 166 " --> pdb=" O GLN N 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 33 Processing helix chain 'O' and resid 84 through 104 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 205 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 121 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) Processing helix chain 'P' and resid 166 through 175 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 'P' and resid 222 through 225 No H-bonds generated for 'chain 'P' and resid 222 through 225' 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 81 through 101 removed outlier: 4.314A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) 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 117 Processing helix chain 'R' and resid 165 through 173 Processing helix chain 'R' and resid 185 through 197 removed outlier: 4.060A pdb=" N LEU R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 229 removed outlier: 3.590A pdb=" N LYS R 227 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL R 229 " --> pdb=" O GLU R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 234 No H-bonds generated for 'chain 'R' and resid 231 through 234' 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 117 removed outlier: 3.775A pdb=" N VAL S 116 " --> pdb=" O VAL S 112 " (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 195 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 29 removed outlier: 3.848A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (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 173 through 178 Processing helix chain 'U' and resid 181 through 183 No H-bonds generated for 'chain 'U' and resid 181 through 183' 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 139 removed outlier: 4.360A pdb=" N GLY V 137 " --> 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 131 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 152 through 165 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 95 Processing helix chain 'X' and resid 146 through 149 No H-bonds generated for 'chain 'X' and resid 146 through 149' 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 50 through 71 removed outlier: 3.613A pdb=" N THR Y 53 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN Y 55 " --> pdb=" O ASP Y 52 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE Y 56 " --> pdb=" O THR Y 53 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU Y 58 " --> pdb=" O GLN Y 55 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS Y 62 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN Y 65 " --> pdb=" O LYS Y 62 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR Y 67 " --> pdb=" O VAL Y 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN Y 71 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 92 Processing helix chain 'Y' and resid 135 through 146 removed outlier: 3.697A pdb=" N THR Y 139 " --> pdb=" O ALA Y 136 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU Y 140 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER Y 141 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU Y 143 " --> pdb=" O LEU Y 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP Y 144 " --> pdb=" O SER Y 141 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR Y 146 " --> pdb=" O LEU Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 169 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 69 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 164 Processing helix chain 'a' and resid 58 through 78 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 97 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 101 Processing helix chain 'b' and resid 146 through 154 removed outlier: 3.905A pdb=" N VAL b 153 " --> pdb=" O LEU b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 162 through 172 removed outlier: 3.729A pdb=" N ARG b 166 " --> pdb=" O GLN b 162 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 167 through 169 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.678A pdb=" N GLY A 142 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS A 78 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS A 71 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET A 80 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 69 " --> pdb=" O MET A 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 159 through 162 Processing sheet with id= D, first strand: chain 'B' and resid 154 through 156 removed outlier: 3.784A pdb=" N THR B 68 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 73 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= F, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 69 through 74 removed outlier: 3.569A pdb=" N ILE D 133 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 167 through 170 removed outlier: 3.757A pdb=" N ARG E 168 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL E 50 " --> pdb=" O GLU E 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 67 through 69 Processing sheet with id= K, first strand: chain 'F' and resid 159 through 161 removed outlier: 3.728A pdb=" N VAL F 215 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 63 through 65 removed outlier: 4.713A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN F 146 " --> pdb=" O PHE F 154 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 45 through 49 Processing sheet with id= N, first strand: chain 'G' and resid 74 through 78 Processing sheet with id= O, first strand: chain 'H' and resid 125 through 128 Processing sheet with id= P, first strand: chain 'H' and resid 45 through 47 Processing sheet with id= Q, first strand: chain 'I' and resid 124 through 127 removed outlier: 4.005A pdb=" N LEU I 175 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU I 186 " --> pdb=" O LEU I 175 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 42 through 46 removed outlier: 3.659A pdb=" N ASP I 104 " --> pdb=" O GLY I 107 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER I 118 " --> pdb=" O TYR I 114 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.232A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 10 through 14 Processing sheet with id= U, first strand: chain 'J' and resid 49 through 54 Processing sheet with id= V, first strand: chain 'J' and resid 27 through 29 removed outlier: 3.759A pdb=" N PHE J 27 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR J 35 " --> pdb=" O PHE J 27 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE J 29 " --> pdb=" O MET J 33 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'K' and resid 129 through 132 Processing sheet with id= X, first strand: chain 'K' and resid 113 through 118 removed outlier: 3.715A pdb=" N ILE K 42 " --> pdb=" O SER K 39 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU K 44 " --> pdb=" O LYS K 37 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS K 37 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS K 46 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET K 35 " --> pdb=" O CYS K 46 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= Z, first strand: chain 'L' and resid 98 through 103 Processing sheet with id= AA, first strand: chain 'M' and resid 135 through 138 Processing sheet with id= AB, first strand: chain 'M' and resid 52 through 55 Processing sheet with id= AC, first strand: chain 'M' and resid 197 through 199 Processing sheet with id= AD, first strand: chain 'N' and resid 136 through 138 removed outlier: 3.674A pdb=" N ALA N 23 " --> pdb=" O LEU N 12 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 42 through 44 Processing sheet with id= AF, first strand: chain 'O' and resid 167 through 169 Processing sheet with id= AG, first strand: chain 'O' and resid 160 through 162 removed outlier: 3.678A pdb=" N GLY O 142 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS O 78 " --> pdb=" O LYS O 71 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS O 71 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET O 80 " --> pdb=" O LEU O 69 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU O 69 " --> pdb=" O MET O 80 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'P' and resid 159 through 162 Processing sheet with id= AI, first strand: chain 'P' and resid 154 through 156 removed outlier: 3.784A pdb=" N THR P 68 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU P 73 " --> pdb=" O PRO P 66 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id= AK, first strand: chain 'Q' and resid 72 through 76 Processing sheet with id= AL, first strand: chain 'R' and resid 158 through 161 Processing sheet with id= AM, first strand: chain 'R' and resid 69 through 74 removed outlier: 3.569A pdb=" N ILE R 133 " --> pdb=" O TYR R 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'S' and resid 167 through 170 removed outlier: 3.757A pdb=" N ARG S 168 " --> pdb=" O GLY S 39 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL S 50 " --> pdb=" O GLU S 216 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'S' and resid 67 through 69 Processing sheet with id= AP, first strand: chain 'T' and resid 159 through 161 removed outlier: 3.729A pdb=" N VAL T 215 " --> pdb=" O ALA T 44 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'T' and resid 63 through 65 removed outlier: 4.713A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS T 156 " --> pdb=" O ILE T 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN T 146 " --> pdb=" O PHE T 154 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'U' and resid 45 through 49 Processing sheet with id= AS, first strand: chain 'U' and resid 74 through 78 Processing sheet with id= AT, first strand: chain 'V' and resid 126 through 128 Processing sheet with id= AU, first strand: chain 'V' and resid 45 through 47 Processing sheet with id= AV, first strand: chain 'W' and resid 124 through 127 removed outlier: 4.005A pdb=" N LEU W 175 " --> pdb=" O LEU W 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU W 186 " --> pdb=" O LEU W 175 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'W' and resid 42 through 46 removed outlier: 3.659A pdb=" N ASP W 104 " --> pdb=" O GLY W 107 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER W 118 " --> pdb=" O TYR W 114 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.232A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'X' and resid 10 through 14 Processing sheet with id= AZ, first strand: chain 'X' and resid 49 through 54 Processing sheet with id= BA, first strand: chain 'X' and resid 27 through 29 removed outlier: 3.759A pdb=" N PHE X 27 " --> pdb=" O THR X 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR X 35 " --> pdb=" O PHE X 27 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE X 29 " --> pdb=" O MET X 33 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET X 33 " --> pdb=" O ILE X 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id= BC, first strand: chain 'Y' and resid 113 through 118 removed outlier: 3.715A pdb=" N ILE Y 42 " --> pdb=" O SER Y 39 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU Y 44 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS Y 37 " --> pdb=" O LEU Y 44 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS Y 46 " --> pdb=" O MET Y 35 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET Y 35 " --> pdb=" O CYS Y 46 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'Z' and resid 5 through 8 Processing sheet with id= BE, first strand: chain 'Z' and resid 98 through 103 Processing sheet with id= BF, first strand: chain 'a' and resid 135 through 138 Processing sheet with id= BG, first strand: chain 'a' and resid 52 through 55 Processing sheet with id= BH, first strand: chain 'a' and resid 197 through 199 Processing sheet with id= BI, first strand: chain 'b' and resid 136 through 138 removed outlier: 3.674A pdb=" N ALA b 23 " --> pdb=" O LEU b 12 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'b' and resid 42 through 44 1835 hydrogen bonds defined for protein. 5058 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: 14.85 Time building geometry restraints manager: 17.08 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: 87.13 - 100.02: 177 100.02 - 112.91: 21518 112.91 - 125.79: 37045 125.79 - 138.68: 875 138.68 - 151.57: 7 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: 10 1.54 - 2.38: 310 2.38 - 3.22: 43722 3.22 - 4.06: 113497 4.06 - 4.90: 213285 Warning: very small nonbonded interaction distances. Nonbonded interactions: 370824 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 2.440 nonbonded pdb=" O VAL J 137 " pdb=" OH TYR J 146 " model vdw 0.977 2.440 nonbonded pdb=" NH1 ARG J 26 " pdb=" CB MET J 33 " model vdw 1.392 3.520 ... (remaining 370819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 0.840 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: 0.040 Extract box with map and model: 6.370 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 104.050 Find NCS groups from input model: 4.210 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.020 ------------------------------------------------------------------------------- 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 : 0.019 0.451 44174 Z= 1.266 Angle : 2.216 38.391 59622 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 : 33.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (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 TRP 0.105 0.015 TRP V 103 HIS 0.008 0.001 HIS T 43 PHE 0.115 0.015 PHE Z 6 TYR 0.135 0.018 TYR M 188 ARG 0.010 0.001 ARG U 129 *********************** 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 fitting. rotamer outliers: 92 poor density : 1872 time to evaluate : 4.530 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 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 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: 0.7371 (mt) REVERT: B 51 GLN cc_start: 0.3953 (OUTLIER) cc_final: 0.2854 (pp30) REVERT: B 207 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.5223 (pp) REVERT: B 213 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6221 (m-40) REVERT: D 153 TYR cc_start: 0.7334 (p90) cc_final: 0.7117 (p90) REVERT: E 21 LEU cc_start: 0.6569 (mt) cc_final: 0.6309 (mp) REVERT: E 70 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8358 (mm) REVERT: H 186 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5133 (mtt180) REVERT: I 126 THR cc_start: 0.8572 (p) cc_final: 0.8158 (m) REVERT: I 139 GLU cc_start: 0.5315 (tt0) cc_final: 0.5107 (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: 0.6999 (tpt) REVERT: K 14 LEU cc_start: 0.7694 (tp) cc_final: 0.7231 (tt) REVERT: M 15 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.5140 (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: 0.7541 (pp) REVERT: M 74 MET cc_start: 0.6047 (mtt) cc_final: 0.5768 (mtp) REVERT: M 173 ARG cc_start: 0.4914 (tpp-160) cc_final: 0.4590 (mtp85) REVERT: N 199 ILE cc_start: 0.5885 (mt) cc_final: 0.5663 (mp) REVERT: O 32 ILE cc_start: 0.7672 (mt) cc_final: 0.7346 (mt) REVERT: O 104 LYS cc_start: 0.7686 (mtpt) cc_final: 0.7315 (mtpt) REVERT: O 170 VAL cc_start: 0.6289 (t) cc_final: 0.6088 (t) REVERT: P 51 GLN cc_start: 0.3948 (OUTLIER) cc_final: 0.2846 (pp30) REVERT: P 213 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6225 (m-40) REVERT: R 153 TYR cc_start: 0.7356 (p90) cc_final: 0.7131 (p90) REVERT: S 21 LEU cc_start: 0.6623 (mt) cc_final: 0.6378 (mp) REVERT: S 70 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8350 (mm) REVERT: V 186 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5147 (mtt180) REVERT: W 24 MET cc_start: 0.5936 (mmt) cc_final: 0.5628 (mmt) REVERT: W 126 THR cc_start: 0.8592 (p) cc_final: 0.8170 (m) REVERT: X 134 ASP cc_start: 0.5616 (p0) cc_final: 0.5227 (p0) REVERT: X 170 MET cc_start: 0.7293 (tpt) cc_final: 0.7031 (tpt) REVERT: Y 14 LEU cc_start: 0.7678 (tp) cc_final: 0.7212 (tt) REVERT: a 15 ILE cc_start: 0.5396 (OUTLIER) cc_final: 0.5128 (pt) REVERT: a 28 ARG cc_start: 0.5748 (ptt180) cc_final: 0.5275 (ptm160) REVERT: a 72 LEU cc_start: 0.7829 (pp) cc_final: 0.7550 (pp) REVERT: a 74 MET cc_start: 0.6053 (mtt) cc_final: 0.5801 (mtp) outliers start: 92 outliers final: 30 residues processed: 1930 average time/residue: 0.5940 time to fit residues: 1800.1174 Evaluate side-chains 1438 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1397 time to evaluate : 4.913 ------------------------------------------------------------------------------- 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 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 459 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 426 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 259 optimal weight: 0.9990 chunk 317 optimal weight: 4.9990 chunk 494 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 A 123 GLN A 127 GLN B 51 GLN B 62 HIS B 87 HIS ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 69 ASN C 142 HIS C 166 ASN D 23 GLN D 54 GLN D 175 ASN E 178 GLN E 211 ASN E 224 GLN F 20 HIS ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 117 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS H 7 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN J 168 GLN J 187 HIS K 55 GLN K 63 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN M 131 GLN N 108 ASN N 147 GLN O 33 ASN O 68 HIS O 90 GLN ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN P 62 HIS P 87 HIS ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Q 30 HIS Q 69 ASN Q 142 HIS Q 166 ASN R 23 GLN R 54 GLN R 175 ASN S 178 GLN S 211 ASN S 224 GLN T 20 HIS ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 HIS T 117 GLN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 156 ASN X 168 GLN X 187 HIS ** Y 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN a 131 GLN b 104 ASN b 108 ASN b 147 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 44174 Z= 0.359 Angle : 0.866 16.351 59622 Z= 0.459 Chirality : 0.051 0.251 6732 Planarity : 0.007 0.081 7614 Dihedral : 10.827 144.028 6324 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.35 % Rotamer: Outliers : 6.14 % Allowed : 16.78 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 5432 helix: -0.95 (0.10), residues: 1890 sheet: -2.12 (0.13), residues: 1276 loop : -1.45 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP b 91 HIS 0.010 0.002 HIS H 66 PHE 0.044 0.003 PHE b 16 TYR 0.034 0.003 TYR K 117 ARG 0.014 0.001 ARG Z 141 *********************** 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 1763 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1480 time to evaluate : 4.956 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: "THR J 196 " (corrupted residue). Skipping it. 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: "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 26 GLU cc_start: 0.5141 (pt0) cc_final: 0.4893 (pt0) REVERT: A 76 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6545 (mp) REVERT: B 94 GLN cc_start: 0.6374 (mm110) cc_final: 0.6084 (mm-40) REVERT: B 139 ASN cc_start: 0.4031 (m-40) cc_final: 0.3745 (m-40) REVERT: B 207 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5817 (pp) REVERT: D 94 HIS cc_start: 0.7551 (t-90) cc_final: 0.7058 (t-90) REVERT: E 86 LYS cc_start: 0.6660 (ttpt) cc_final: 0.6246 (mtpt) REVERT: F 18 ARG cc_start: 0.4822 (mpp-170) cc_final: 0.4153 (mpp-170) REVERT: F 132 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7807 (mp) REVERT: G 167 LYS cc_start: 0.6111 (OUTLIER) cc_final: 0.5793 (pttt) REVERT: H 92 GLU cc_start: 0.6119 (pm20) cc_final: 0.5790 (pm20) REVERT: H 142 THR cc_start: 0.6815 (m) cc_final: 0.5646 (p) REVERT: I 83 LEU cc_start: 0.6704 (mt) cc_final: 0.6492 (mt) REVERT: L 55 TRP cc_start: 0.6948 (m100) cc_final: 0.6694 (m100) REVERT: L 143 TYR cc_start: 0.7408 (t80) cc_final: 0.6924 (t80) REVERT: M 28 ARG cc_start: 0.5870 (ptt180) cc_final: 0.4968 (ptm160) REVERT: N 38 ASN cc_start: 0.5910 (t0) cc_final: 0.5699 (t0) REVERT: N 76 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6279 (pp) REVERT: N 147 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7422 (tp40) REVERT: O 26 GLU cc_start: 0.5209 (pt0) cc_final: 0.4980 (pt0) REVERT: O 76 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6551 (mp) REVERT: P 139 ASN cc_start: 0.4083 (m-40) cc_final: 0.3761 (m-40) REVERT: R 94 HIS cc_start: 0.7556 (t-90) cc_final: 0.7125 (t-90) REVERT: S 86 LYS cc_start: 0.6673 (ttpt) cc_final: 0.6254 (mtpt) REVERT: T 16 GLN cc_start: 0.5551 (OUTLIER) cc_final: 0.4594 (mp10) REVERT: T 132 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7843 (mp) REVERT: U 167 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5821 (pttt) REVERT: V 92 GLU cc_start: 0.6108 (pm20) cc_final: 0.5772 (pm20) REVERT: V 142 THR cc_start: 0.6843 (m) cc_final: 0.5692 (p) REVERT: W 83 LEU cc_start: 0.6736 (mt) cc_final: 0.6505 (mt) REVERT: Z 55 TRP cc_start: 0.6945 (m100) cc_final: 0.6688 (m100) REVERT: Z 143 TYR cc_start: 0.7421 (t80) cc_final: 0.6906 (t80) REVERT: b 76 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6274 (pp) outliers start: 283 outliers final: 161 residues processed: 1648 average time/residue: 0.5790 time to fit residues: 1513.7134 Evaluate side-chains 1494 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1322 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 123 GLN 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 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 207 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 41 ASP 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 42 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 135 PHE 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 13 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR 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 37 ILE Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 125 VAL 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 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 51 ASP 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 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 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 126 ASP 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 51 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 112 ASP 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 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 180 ASP 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 41 ASP 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 42 VAL Chi-restraints excluded: chain R residue 68 ASN 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 79 ASP Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 227 HIS Chi-restraints excluded: chain T residue 16 GLN Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 118 ILE Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 135 PHE 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 13 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 169 SER 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 58 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 125 VAL 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 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 184 ASP Chi-restraints excluded: chain Z residue 51 ASP 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 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 126 ASP 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 274 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 411 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 494 optimal weight: 6.9990 chunk 534 optimal weight: 5.9990 chunk 440 optimal weight: 9.9990 chunk 490 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 397 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 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** D 175 ASN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN N 104 ASN O 33 ASN ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 94 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 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN ** R 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN W 57 GLN ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN b 104 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 44174 Z= 0.320 Angle : 0.787 15.958 59622 Z= 0.414 Chirality : 0.048 0.239 6732 Planarity : 0.006 0.062 7614 Dihedral : 10.231 138.958 6274 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.23 % Favored : 95.60 % Rotamer: Outliers : 7.18 % Allowed : 19.64 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 5432 helix: -0.68 (0.11), residues: 1894 sheet: -1.98 (0.13), residues: 1248 loop : -1.49 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 91 HIS 0.011 0.002 HIS H 66 PHE 0.042 0.003 PHE b 16 TYR 0.027 0.002 TYR V 61 ARG 0.012 0.001 ARG L 141 *********************** 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 1718 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1387 time to evaluate : 4.781 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 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: "ILE O 235 " (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 TARDY: cannot create tardy model for: "THR X 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 GLN cc_start: 0.6275 (mm110) cc_final: 0.6024 (mm-40) REVERT: B 207 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5503 (pp) REVERT: C 12 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: C 119 GLN cc_start: 0.5919 (tp-100) cc_final: 0.5656 (tp-100) REVERT: E 51 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5553 (tm-30) REVERT: F 18 ARG cc_start: 0.5100 (mpp-170) cc_final: 0.4446 (mpp-170) REVERT: F 132 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7710 (mp) REVERT: G 167 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5854 (pptt) REVERT: I 135 MET cc_start: 0.6315 (mmm) cc_final: 0.6037 (mmm) REVERT: N 5 MET cc_start: 0.5882 (mmt) cc_final: 0.5655 (mmt) REVERT: N 76 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6159 (pp) REVERT: Q 12 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: Q 119 GLN cc_start: 0.5911 (tp-100) cc_final: 0.5642 (tp-100) REVERT: R 153 TYR cc_start: 0.6880 (p90) cc_final: 0.6651 (p90) REVERT: S 51 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.5530 (tm-30) REVERT: T 16 GLN cc_start: 0.5334 (OUTLIER) cc_final: 0.4180 (mp10) REVERT: T 18 ARG cc_start: 0.5686 (mpp-170) cc_final: 0.5004 (mpt90) REVERT: T 132 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7810 (mp) REVERT: U 167 LYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5859 (pttt) REVERT: W 135 MET cc_start: 0.6371 (mmm) cc_final: 0.6056 (mmm) REVERT: W 186 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4066 (mt) REVERT: X 37 ASP cc_start: 0.7427 (t0) cc_final: 0.7148 (t0) REVERT: b 76 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6156 (pp) outliers start: 331 outliers final: 221 residues processed: 1599 average time/residue: 0.5623 time to fit residues: 1439.7510 Evaluate side-chains 1528 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1294 time to evaluate : 4.700 ------------------------------------------------------------------------------- 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 79 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 235 ILE 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 148 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 ILE 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 41 ASP Chi-restraints excluded: chain C residue 44 LEU 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 133 SER Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 68 ASN 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 152 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL 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 77 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 174 ARG 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 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 134 ASP 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 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 42 LEU 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 L residue 138 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 133 ASP 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 126 ASP 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 N residue 193 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 235 ILE 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 167 VAL Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 191 ILE 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 41 ASP Chi-restraints excluded: chain Q residue 44 LEU 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 133 SER Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 68 ASN 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 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain T residue 10 VAL 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 47 VAL 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 T residue 159 MET Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 174 ARG 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 199 ILE Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 8 PHE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 174 ILE 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 38 SER Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 134 ASP 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 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 184 ASP Chi-restraints excluded: chain Z residue 42 LEU 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 Z residue 141 ARG Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 133 ASP 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 126 ASP 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 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 488 optimal weight: 7.9990 chunk 372 optimal weight: 0.9990 chunk 256 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 496 optimal weight: 5.9990 chunk 525 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 chunk 470 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 127 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 168 ASN C 102 GLN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN N 147 GLN O 33 ASN O 75 ASN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 GLN P 168 ASN Q 102 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN U 22 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN b 147 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 44174 Z= 0.231 Angle : 0.694 16.115 59622 Z= 0.362 Chirality : 0.046 0.247 6732 Planarity : 0.005 0.054 7614 Dihedral : 9.699 135.202 6270 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Rotamer: Outliers : 6.46 % Allowed : 21.81 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.11), residues: 5432 helix: -0.33 (0.11), residues: 1904 sheet: -1.83 (0.13), residues: 1244 loop : -1.38 (0.13), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 91 HIS 0.008 0.001 HIS V 66 PHE 0.030 0.002 PHE L 54 TYR 0.024 0.002 TYR I 111 ARG 0.006 0.001 ARG N 44 *********************** 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 1642 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1344 time to evaluate : 5.094 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 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: A 76 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6134 (mp) REVERT: A 108 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.5056 (tm-30) REVERT: B 195 LYS cc_start: 0.4891 (mmmt) cc_final: 0.4535 (mmmt) REVERT: B 207 ILE cc_start: 0.5793 (OUTLIER) cc_final: 0.5448 (pp) REVERT: B 218 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.6110 (mtp180) REVERT: C 12 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: F 18 ARG cc_start: 0.4817 (mpp-170) cc_final: 0.4241 (mpp-170) REVERT: F 132 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7743 (mp) REVERT: G 167 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5853 (pttt) REVERT: G 169 ARG cc_start: 0.5618 (tpt90) cc_final: 0.5319 (tpt90) REVERT: L 91 LYS cc_start: 0.5780 (tttp) cc_final: 0.5550 (tttp) REVERT: M 148 LEU cc_start: 0.4995 (tt) cc_final: 0.4335 (tp) REVERT: O 76 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6141 (mp) REVERT: O 108 GLU cc_start: 0.5369 (OUTLIER) cc_final: 0.5072 (tm-30) REVERT: P 195 LYS cc_start: 0.4854 (mmmt) cc_final: 0.4515 (mmmt) REVERT: P 218 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.6109 (mtp180) REVERT: Q 12 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: R 153 TYR cc_start: 0.7013 (p90) cc_final: 0.6746 (p90) REVERT: T 16 GLN cc_start: 0.4969 (OUTLIER) cc_final: 0.4320 (mp10) REVERT: T 18 ARG cc_start: 0.5575 (mpp-170) cc_final: 0.5000 (mpt90) REVERT: T 132 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7759 (mp) REVERT: U 167 LYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5836 (pttt) REVERT: Z 91 LYS cc_start: 0.5794 (tttp) cc_final: 0.5547 (tttp) REVERT: a 66 LYS cc_start: 0.8238 (mtmm) cc_final: 0.8030 (mtmm) REVERT: a 83 MET cc_start: 0.5964 (tpp) cc_final: 0.5764 (tpp) REVERT: a 148 LEU cc_start: 0.4987 (tt) cc_final: 0.4330 (tp) outliers start: 298 outliers final: 205 residues processed: 1536 average time/residue: 0.5758 time to fit residues: 1414.3778 Evaluate side-chains 1498 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1279 time to evaluate : 4.984 ------------------------------------------------------------------------------- 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 79 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 113 MET 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 148 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 44 LEU 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 134 LEU Chi-restraints excluded: chain C residue 151 ASP 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 42 VAL 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 152 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL 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 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 132 LEU 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 G residue 167 LYS Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 164 MET 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 76 VAL 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 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 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 184 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 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 147 GLN 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 N residue 193 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR 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 218 ARG Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 LEU 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 134 LEU Chi-restraints excluded: chain Q residue 151 ASP 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 42 VAL 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 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL 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 16 GLN Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 32 ASN 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 167 LYS Chi-restraints excluded: chain U residue 211 LEU Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 220 THR Chi-restraints excluded: chain V residue 3 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 46 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 169 SER 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 63 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 121 CYS 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 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 184 ASP 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 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 126 ASP 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 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 437 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 391 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 chunk 448 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 268 optimal weight: 0.7980 chunk 471 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 127 GLN B 108 GLN D 215 GLN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 215 GLN ** S 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN b 147 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44174 Z= 0.218 Angle : 0.680 16.123 59622 Z= 0.353 Chirality : 0.045 0.261 6732 Planarity : 0.005 0.053 7614 Dihedral : 9.358 133.606 6270 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.80 % Rotamer: Outliers : 6.72 % Allowed : 22.68 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.11), residues: 5432 helix: -0.19 (0.11), residues: 1904 sheet: -1.73 (0.13), residues: 1244 loop : -1.29 (0.13), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 91 HIS 0.007 0.001 HIS S 227 PHE 0.037 0.002 PHE P 172 TYR 0.029 0.002 TYR V 90 ARG 0.014 0.000 ARG L 120 *********************** 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 1668 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1358 time to evaluate : 4.816 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 revert: symmetry clash 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: A 76 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6141 (mp) REVERT: A 108 GLU cc_start: 0.5223 (OUTLIER) cc_final: 0.4958 (tm-30) REVERT: B 207 ILE cc_start: 0.5721 (OUTLIER) cc_final: 0.5399 (pp) REVERT: C 12 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: F 18 ARG cc_start: 0.4857 (mpp-170) cc_final: 0.4251 (mpp-170) REVERT: F 87 PHE cc_start: 0.6668 (t80) cc_final: 0.6438 (t80) REVERT: F 132 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7655 (mp) REVERT: H 45 ARG cc_start: 0.5986 (ptp90) cc_final: 0.5102 (ptp90) REVERT: H 147 MET cc_start: 0.5443 (mtt) cc_final: 0.5149 (ttm) REVERT: I 203 ARG cc_start: 0.5454 (mmt90) cc_final: 0.4764 (ptm-80) REVERT: K 85 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6748 (ttp80) REVERT: M 28 ARG cc_start: 0.5957 (ptt180) cc_final: 0.5140 (ptm160) REVERT: M 148 LEU cc_start: 0.5140 (tt) cc_final: 0.4529 (tp) REVERT: N 76 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5974 (pp) REVERT: N 186 ARG cc_start: 0.5304 (ptm160) cc_final: 0.4857 (tpm170) REVERT: O 76 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6127 (mp) REVERT: O 108 GLU cc_start: 0.5242 (OUTLIER) cc_final: 0.4935 (tm-30) REVERT: P 108 GLN cc_start: 0.7414 (mm110) cc_final: 0.7143 (mm-40) REVERT: P 195 LYS cc_start: 0.4984 (mmmt) cc_final: 0.4641 (mmmt) REVERT: Q 12 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: Q 35 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6718 (pp) REVERT: R 153 TYR cc_start: 0.7066 (p90) cc_final: 0.6842 (p90) REVERT: T 16 GLN cc_start: 0.4791 (OUTLIER) cc_final: 0.4087 (mp10) REVERT: T 18 ARG cc_start: 0.5375 (mpp-170) cc_final: 0.4852 (mpt90) REVERT: T 87 PHE cc_start: 0.6656 (t80) cc_final: 0.6446 (t80) REVERT: T 132 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7668 (mp) REVERT: V 45 ARG cc_start: 0.6023 (ptp90) cc_final: 0.5127 (ptp90) REVERT: W 203 ARG cc_start: 0.5414 (mmt90) cc_final: 0.4699 (ptm-80) REVERT: Y 85 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6765 (ttp80) REVERT: a 28 ARG cc_start: 0.5985 (ptt180) cc_final: 0.5024 (ptm-80) REVERT: a 66 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7978 (mtmm) REVERT: a 148 LEU cc_start: 0.5141 (tt) cc_final: 0.4339 (tp) REVERT: b 5 MET cc_start: 0.5959 (mmt) cc_final: 0.5725 (mmt) REVERT: b 76 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.5977 (pp) REVERT: b 186 ARG cc_start: 0.5355 (ptm160) cc_final: 0.4890 (tpm170) outliers start: 310 outliers final: 227 residues processed: 1555 average time/residue: 0.5671 time to fit residues: 1406.2590 Evaluate side-chains 1514 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1272 time to evaluate : 4.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 44 LEU 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 134 LEU Chi-restraints excluded: chain C residue 151 ASP 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 42 VAL 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 152 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 13 ASN 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 114 GLN Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL 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 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 174 ARG 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 218 GLU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 3 ILE 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 46 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 MET 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 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 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 65 ARG 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 192 ASP Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU 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 184 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 122 SER Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 126 ASP 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 N residue 193 THR Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 196 GLU 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 140 GLU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 LEU 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 133 SER Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 151 ASP 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 42 VAL 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 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 13 ASN 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 114 GLN Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL 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 16 GLN 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 66 VAL Chi-restraints excluded: chain T residue 73 SER 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 T residue 138 ASP Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 174 ARG Chi-restraints excluded: chain U residue 32 ASN 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 3 ILE 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 46 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 169 SER 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 83 LEU Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 178 ILE 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 149 CYS Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 85 ARG Chi-restraints excluded: chain Y residue 184 ASP 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 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 141 ARG Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 104 ASN Chi-restraints excluded: chain b residue 126 ASP 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 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 176 optimal weight: 10.0000 chunk 473 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 308 optimal weight: 0.0030 chunk 129 optimal weight: 20.0000 chunk 526 optimal weight: 20.0000 chunk 436 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- 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** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN E 104 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 110 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN S 104 ASN ** S 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 GLN U 221 ASN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 147 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 44174 Z= 0.295 Angle : 0.728 16.231 59622 Z= 0.379 Chirality : 0.047 0.300 6732 Planarity : 0.005 0.123 7614 Dihedral : 9.324 133.337 6268 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 7.33 % Allowed : 24.02 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.11), residues: 5432 helix: -0.33 (0.11), residues: 1900 sheet: -1.67 (0.14), residues: 1248 loop : -1.36 (0.13), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 91 HIS 0.009 0.002 HIS V 66 PHE 0.039 0.003 PHE P 172 TYR 0.029 0.002 TYR W 111 ARG 0.005 0.001 ARG R 81 *********************** 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 1635 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1297 time to evaluate : 4.977 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 revert: symmetry clash 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. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 ILE cc_start: 0.5913 (OUTLIER) cc_final: 0.5469 (pp) REVERT: C 12 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: D 127 PHE cc_start: 0.7230 (m-10) cc_final: 0.7024 (m-10) REVERT: F 132 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7742 (mp) REVERT: G 22 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7952 (tp40) REVERT: H 147 MET cc_start: 0.5424 (mtt) cc_final: 0.5203 (ttm) REVERT: I 203 ARG cc_start: 0.5440 (mmt90) cc_final: 0.4729 (ptm-80) REVERT: K 154 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.5412 (mm-30) REVERT: M 28 ARG cc_start: 0.6090 (ptt180) cc_final: 0.5222 (ptm160) REVERT: N 5 MET cc_start: 0.5824 (mmt) cc_final: 0.5558 (mmt) REVERT: N 76 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.5980 (pp) REVERT: N 186 ARG cc_start: 0.5616 (ptm160) cc_final: 0.4901 (tpm170) REVERT: P 108 GLN cc_start: 0.7421 (mm110) cc_final: 0.7164 (mm-40) REVERT: Q 12 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: Q 35 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6949 (pp) REVERT: R 127 PHE cc_start: 0.7251 (m-10) cc_final: 0.7037 (m-10) REVERT: R 153 TYR cc_start: 0.7116 (p90) cc_final: 0.6850 (p90) REVERT: T 18 ARG cc_start: 0.5467 (mpp-170) cc_final: 0.4959 (mpt90) REVERT: T 132 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7725 (mp) REVERT: W 186 LEU cc_start: 0.5380 (OUTLIER) cc_final: 0.4548 (mt) REVERT: W 203 ARG cc_start: 0.5502 (mmt90) cc_final: 0.4688 (ptm-80) REVERT: Y 154 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5417 (mm-30) REVERT: a 28 ARG cc_start: 0.6071 (ptt180) cc_final: 0.5091 (ptm-80) REVERT: b 5 MET cc_start: 0.5893 (mmt) cc_final: 0.5669 (mmt) REVERT: b 76 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6100 (pp) REVERT: b 147 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7482 (tp40) REVERT: b 186 ARG cc_start: 0.5668 (ptm160) cc_final: 0.4982 (tpm170) outliers start: 338 outliers final: 268 residues processed: 1519 average time/residue: 0.5691 time to fit residues: 1381.7903 Evaluate side-chains 1525 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1244 time to evaluate : 4.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 VAL 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 207 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 151 ASP 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 42 VAL Chi-restraints excluded: chain D residue 68 ASN 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 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL 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 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 37 ILE 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 220 THR Chi-restraints excluded: chain H residue 3 ILE 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 46 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 164 MET 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 38 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU 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 57 THR Chi-restraints excluded: chain J residue 65 ARG Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 CYS 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 14 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 184 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 102 CYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 126 ASP 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 N residue 193 THR Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL 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 207 SER Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 140 GLU Chi-restraints excluded: chain P residue 144 TYR Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 LEU 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 133 SER Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 151 ASP 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 42 VAL Chi-restraints excluded: chain R residue 68 ASN 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 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL 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 66 VAL Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 138 ASP Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 174 ARG Chi-restraints excluded: chain U residue 37 ILE 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 U residue 220 THR Chi-restraints excluded: chain V residue 3 ILE 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 46 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain V residue 169 SER 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 38 SER Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 83 LEU 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 57 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 121 CYS 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 14 LEU Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Y residue 184 ASP 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 102 CYS Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 126 ASP 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 159 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 507 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 299 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 297 optimal weight: 9.9990 chunk 443 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 524 optimal weight: 0.9990 chunk 328 optimal weight: 7.9990 chunk 319 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 44174 Z= 0.312 Angle : 0.755 16.236 59622 Z= 0.391 Chirality : 0.048 0.257 6732 Planarity : 0.006 0.109 7614 Dihedral : 9.293 133.305 6266 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 7.74 % Allowed : 24.48 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.11), residues: 5432 helix: -0.46 (0.11), residues: 1908 sheet: -1.69 (0.13), residues: 1250 loop : -1.43 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 91 HIS 0.012 0.002 HIS H 66 PHE 0.040 0.003 PHE B 172 TYR 0.032 0.002 TYR Z 88 ARG 0.014 0.001 ARG U 232 *********************** 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 1622 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 1265 time to evaluate : 3.904 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 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 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: "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 TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 207 ILE cc_start: 0.6169 (OUTLIER) cc_final: 0.5684 (pp) REVERT: C 12 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: F 132 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7803 (mp) REVERT: H 147 MET cc_start: 0.5477 (mtt) cc_final: 0.5210 (ttm) REVERT: I 203 ARG cc_start: 0.5401 (mmt90) cc_final: 0.4620 (ptm-80) REVERT: J 116 PHE cc_start: 0.4215 (OUTLIER) cc_final: 0.4010 (t80) REVERT: K 85 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6654 (ttp80) REVERT: K 154 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5520 (mm-30) REVERT: M 28 ARG cc_start: 0.6140 (ptt180) cc_final: 0.5138 (ptm-80) REVERT: M 66 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7813 (mtmm) REVERT: N 5 MET cc_start: 0.5858 (mmt) cc_final: 0.5538 (mmt) REVERT: N 76 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6187 (pp) REVERT: N 77 LEU cc_start: 0.6610 (mt) cc_final: 0.6260 (mt) REVERT: P 94 GLN cc_start: 0.6325 (mm110) cc_final: 0.6104 (mm-40) REVERT: P 108 GLN cc_start: 0.7429 (mm110) cc_final: 0.7152 (mm-40) REVERT: Q 12 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: Q 25 MET cc_start: 0.6297 (mmp) cc_final: 0.6035 (mmp) REVERT: Q 35 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6981 (pp) REVERT: R 153 TYR cc_start: 0.7105 (p90) cc_final: 0.6896 (p90) REVERT: T 18 ARG cc_start: 0.5344 (mpp-170) cc_final: 0.4907 (mpt90) REVERT: T 132 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7704 (mp) REVERT: U 129 ARG cc_start: 0.8130 (ptt90) cc_final: 0.7847 (ptt90) REVERT: V 19 ARG cc_start: 0.7219 (mtp180) cc_final: 0.6812 (mtp180) REVERT: W 186 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.4718 (mt) REVERT: W 203 ARG cc_start: 0.5457 (mmt90) cc_final: 0.4592 (ptm-80) REVERT: Y 85 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6683 (ttp80) REVERT: Y 154 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5522 (mm-30) REVERT: a 28 ARG cc_start: 0.6135 (ptt180) cc_final: 0.5096 (ptm-80) REVERT: b 5 MET cc_start: 0.5897 (mmt) cc_final: 0.5617 (mmt) REVERT: b 76 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6182 (pp) REVERT: b 77 LEU cc_start: 0.6598 (mt) cc_final: 0.6232 (mt) outliers start: 357 outliers final: 283 residues processed: 1510 average time/residue: 0.5551 time to fit residues: 1341.7626 Evaluate side-chains 1532 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1235 time to evaluate : 4.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 151 ASP 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 42 VAL Chi-restraints excluded: chain D residue 68 ASN 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 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 205 VAL 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 229 PHE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 22 GLN 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 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 3 ILE 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 34 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 164 MET 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 37 ILE Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU 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 57 THR Chi-restraints excluded: chain J residue 65 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 121 CYS 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 14 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 184 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 102 CYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 140 GLU Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 151 ASP 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 42 VAL Chi-restraints excluded: chain R residue 68 ASN 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 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 205 VAL 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 229 PHE 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 66 VAL Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 138 ASP Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 174 ARG Chi-restraints excluded: chain U residue 37 ILE 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 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 220 THR Chi-restraints excluded: chain V residue 3 ILE 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 46 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain V residue 169 SER 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 38 SER Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 83 LEU 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 57 THR 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 121 CYS 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 14 LEU Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 85 ARG Chi-restraints excluded: chain Y residue 151 ILE Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 184 ASP 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 102 CYS Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 141 ARG Chi-restraints excluded: chain Z residue 154 ASP Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 126 ASP 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 163 THR Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 324 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 333 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 259 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 412 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 110 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS N 147 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 117 GLN ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 82 ASN a 77 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 44174 Z= 0.233 Angle : 0.704 15.915 59622 Z= 0.363 Chirality : 0.046 0.286 6732 Planarity : 0.005 0.148 7614 Dihedral : 8.961 131.491 6266 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.33 % Favored : 95.54 % Rotamer: Outliers : 6.59 % Allowed : 25.80 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.11), residues: 5432 helix: -0.27 (0.11), residues: 1906 sheet: -1.52 (0.14), residues: 1256 loop : -1.31 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 91 HIS 0.009 0.001 HIS V 66 PHE 0.043 0.002 PHE B 172 TYR 0.026 0.002 TYR L 88 ARG 0.013 0.001 ARG U 232 *********************** 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 1600 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1296 time to evaluate : 4.893 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 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 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 TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 207 ILE cc_start: 0.6097 (OUTLIER) cc_final: 0.5670 (pp) REVERT: C 12 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: D 228 TYR cc_start: 0.4587 (OUTLIER) cc_final: 0.4179 (p90) REVERT: F 132 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7675 (mp) REVERT: H 164 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4289 (ptt) REVERT: I 203 ARG cc_start: 0.5336 (mmt90) cc_final: 0.4474 (ptm-80) REVERT: K 154 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5359 (mm-30) REVERT: M 28 ARG cc_start: 0.6095 (ptt180) cc_final: 0.5114 (ptm-80) REVERT: M 66 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7840 (mttp) REVERT: N 5 MET cc_start: 0.5839 (mmt) cc_final: 0.5556 (mmt) REVERT: N 76 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6209 (pp) REVERT: N 77 LEU cc_start: 0.6550 (mt) cc_final: 0.6198 (mt) REVERT: N 186 ARG cc_start: 0.5577 (ptm160) cc_final: 0.5092 (tpt90) REVERT: O 93 ARG cc_start: 0.6668 (mmm-85) cc_final: 0.6424 (mtp180) REVERT: P 108 GLN cc_start: 0.7387 (mm110) cc_final: 0.7105 (mm-40) REVERT: Q 12 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: Q 25 MET cc_start: 0.6238 (mmp) cc_final: 0.5989 (mmp) REVERT: Q 35 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6895 (pp) REVERT: R 228 TYR cc_start: 0.4568 (OUTLIER) cc_final: 0.4175 (p90) REVERT: T 18 ARG cc_start: 0.5370 (mpp-170) cc_final: 0.4940 (mpt90) REVERT: T 132 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7710 (mp) REVERT: U 129 ARG cc_start: 0.8105 (ptt90) cc_final: 0.7844 (ptt90) REVERT: V 65 PHE cc_start: 0.6680 (t80) cc_final: 0.5674 (t80) REVERT: W 186 LEU cc_start: 0.5232 (OUTLIER) cc_final: 0.4455 (mt) REVERT: W 203 ARG cc_start: 0.5430 (mmt90) cc_final: 0.4520 (ptm-80) REVERT: X 93 LEU cc_start: 0.7106 (tp) cc_final: 0.6583 (tt) REVERT: Y 85 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6680 (ttp80) REVERT: Y 154 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5440 (mm-30) REVERT: Z 89 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6921 (tm-30) REVERT: a 28 ARG cc_start: 0.6037 (ptt180) cc_final: 0.5092 (ptm-80) REVERT: a 66 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7808 (mtmm) REVERT: b 5 MET cc_start: 0.5865 (mmt) cc_final: 0.5618 (mmt) REVERT: b 76 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6225 (pp) REVERT: b 77 LEU cc_start: 0.6504 (mt) cc_final: 0.6154 (mt) REVERT: b 147 GLN cc_start: 0.7807 (tp40) cc_final: 0.7400 (tp40) REVERT: b 186 ARG cc_start: 0.5686 (ptm160) cc_final: 0.5154 (tpt90) outliers start: 304 outliers final: 232 residues processed: 1491 average time/residue: 0.5607 time to fit residues: 1335.6577 Evaluate side-chains 1489 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1242 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 VAL 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 235 ILE Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 151 ASP 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 42 VAL 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 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 205 VAL 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 229 PHE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 37 ILE 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 220 THR Chi-restraints excluded: chain H residue 3 ILE 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 46 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 MET 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 38 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU 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 57 THR Chi-restraints excluded: chain J residue 65 ARG Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 CYS 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 14 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 184 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 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 43 MET 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 163 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL 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 235 ILE Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 151 ASP 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 42 VAL 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 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 205 VAL 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 229 PHE Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain U residue 37 ILE 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 U residue 220 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain V residue 169 SER 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 38 SER Chi-restraints excluded: chain W residue 52 THR 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 57 THR 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 121 CYS Chi-restraints excluded: chain X residue 149 CYS Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 85 ARG Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Y residue 184 ASP 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 102 CYS Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 126 ASP 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 163 THR Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 476 optimal weight: 0.8980 chunk 502 optimal weight: 0.3980 chunk 458 optimal weight: 1.9990 chunk 488 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 383 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 441 optimal weight: 7.9990 chunk 462 optimal weight: 7.9990 chunk 486 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN K 24 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN M 77 HIS N 147 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 44174 Z= 0.241 Angle : 0.723 15.879 59622 Z= 0.370 Chirality : 0.047 0.272 6732 Planarity : 0.005 0.136 7614 Dihedral : 8.790 129.558 6265 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 6.11 % Allowed : 26.50 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.11), residues: 5432 helix: -0.24 (0.11), residues: 1904 sheet: -1.43 (0.14), residues: 1260 loop : -1.28 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 153 HIS 0.010 0.001 HIS V 66 PHE 0.044 0.002 PHE B 172 TYR 0.028 0.002 TYR V 136 ARG 0.012 0.001 ARG a 71 *********************** 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 1549 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1267 time to evaluate : 4.617 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: "GLU E 236 " (corrupted residue). Skipping it. 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. 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 TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. REVERT: B 207 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5609 (pp) REVERT: C 12 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: F 132 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7636 (mp) REVERT: H 164 MET cc_start: 0.5136 (OUTLIER) cc_final: 0.4265 (ptt) REVERT: I 186 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4423 (mt) REVERT: I 203 ARG cc_start: 0.5301 (mmt90) cc_final: 0.4457 (ptm-80) REVERT: K 85 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6427 (ttp80) REVERT: K 154 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5462 (mm-30) REVERT: L 74 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6921 (tt) REVERT: M 28 ARG cc_start: 0.6085 (ptt180) cc_final: 0.5211 (ptm160) REVERT: N 76 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6160 (pp) REVERT: N 186 ARG cc_start: 0.5625 (ptm160) cc_final: 0.4774 (tpm170) REVERT: P 108 GLN cc_start: 0.7460 (mm110) cc_final: 0.7187 (mm-40) REVERT: Q 12 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: Q 25 MET cc_start: 0.6211 (mmp) cc_final: 0.5943 (mmp) REVERT: T 18 ARG cc_start: 0.5337 (mpp-170) cc_final: 0.4887 (mpt90) REVERT: T 132 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7670 (mp) REVERT: W 186 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4459 (mt) REVERT: W 203 ARG cc_start: 0.5339 (mmt90) cc_final: 0.4502 (ptm-80) REVERT: X 65 ARG cc_start: 0.5624 (ttt180) cc_final: 0.5414 (ttt180) REVERT: X 69 ARG cc_start: 0.6478 (ttp-170) cc_final: 0.6172 (mtp180) REVERT: X 93 LEU cc_start: 0.6985 (tp) cc_final: 0.6673 (tt) REVERT: Y 85 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6495 (ttp80) REVERT: Y 154 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5442 (mm-30) REVERT: Z 89 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6900 (tm-30) REVERT: a 28 ARG cc_start: 0.6085 (ptt180) cc_final: 0.5257 (ptm160) REVERT: a 66 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7893 (mtmm) REVERT: b 60 PHE cc_start: 0.7205 (t80) cc_final: 0.7000 (t80) REVERT: b 76 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6112 (pp) REVERT: b 147 GLN cc_start: 0.7809 (tp40) cc_final: 0.7444 (tp40) REVERT: b 186 ARG cc_start: 0.5633 (ptm160) cc_final: 0.4761 (tpm170) outliers start: 282 outliers final: 242 residues processed: 1460 average time/residue: 0.5620 time to fit residues: 1313.6758 Evaluate side-chains 1494 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1237 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 VAL 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 235 ILE Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 155 ASN 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 42 VAL 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 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 205 VAL 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 229 PHE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 37 ILE 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 220 THR Chi-restraints excluded: chain H residue 3 ILE 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 46 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 MET 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 38 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU 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 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 14 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 184 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 102 CYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 63 LEU 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 163 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL 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 235 ILE Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 151 ASP 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 42 VAL 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 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 205 VAL 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 229 PHE Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 174 ARG Chi-restraints excluded: chain U residue 37 ILE 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 U residue 220 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 8 PHE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain V residue 169 SER 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 38 SER Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU 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 57 THR 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 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 85 ARG Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Y residue 184 ASP 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 102 CYS Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain a residue 198 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 126 ASP 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 163 THR Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 320 optimal weight: 0.9980 chunk 516 optimal weight: 6.9990 chunk 315 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 359 optimal weight: 20.0000 chunk 541 optimal weight: 0.9990 chunk 498 optimal weight: 6.9990 chunk 431 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 333 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN ** O 24 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** ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 44174 Z= 0.236 Angle : 0.732 15.677 59622 Z= 0.372 Chirality : 0.047 0.287 6732 Planarity : 0.005 0.098 7614 Dihedral : 8.664 127.904 6265 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.49 % Rotamer: Outliers : 5.72 % Allowed : 27.49 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.11), residues: 5432 helix: -0.21 (0.11), residues: 1912 sheet: -1.36 (0.14), residues: 1272 loop : -1.22 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 153 HIS 0.011 0.001 HIS V 66 PHE 0.045 0.002 PHE B 172 TYR 0.032 0.002 TYR Q 136 ARG 0.017 0.001 ARG a 71 ********************** 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 1518 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1254 time to evaluate : 4.820 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: "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 TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. 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: B 134 LEU cc_start: 0.8233 (mt) cc_final: 0.8026 (mt) REVERT: B 207 ILE cc_start: 0.5936 (OUTLIER) cc_final: 0.5477 (pp) REVERT: C 12 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: F 132 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7640 (mp) REVERT: G 181 MET cc_start: 0.6643 (pmm) cc_final: 0.6224 (pmm) REVERT: H 164 MET cc_start: 0.5087 (OUTLIER) cc_final: 0.4265 (ptt) REVERT: I 186 LEU cc_start: 0.5184 (OUTLIER) cc_final: 0.3853 (mt) REVERT: I 203 ARG cc_start: 0.5235 (mmt90) cc_final: 0.4744 (ptm-80) REVERT: J 69 ARG cc_start: 0.6527 (ttp-170) cc_final: 0.6313 (mtp180) REVERT: K 85 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6357 (ttp80) REVERT: L 74 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6888 (tt) REVERT: M 28 ARG cc_start: 0.6112 (ptt180) cc_final: 0.5234 (ptm160) REVERT: N 76 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6136 (pp) REVERT: N 186 ARG cc_start: 0.5536 (ptm160) cc_final: 0.4822 (tpm170) REVERT: P 48 GLU cc_start: 0.5610 (mm-30) cc_final: 0.4065 (mt-10) REVERT: P 108 GLN cc_start: 0.7440 (mm110) cc_final: 0.7226 (mm-40) REVERT: Q 12 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: Q 25 MET cc_start: 0.6192 (mmp) cc_final: 0.5940 (mmp) REVERT: T 18 ARG cc_start: 0.5272 (mpp-170) cc_final: 0.4852 (mpt90) REVERT: T 132 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7669 (mp) REVERT: U 181 MET cc_start: 0.6656 (pmm) cc_final: 0.6236 (pmm) REVERT: W 186 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.4984 (mt) REVERT: W 203 ARG cc_start: 0.5126 (mmt90) cc_final: 0.4081 (mmt-90) REVERT: X 65 ARG cc_start: 0.5838 (ttt180) cc_final: 0.5572 (ttt180) REVERT: X 69 ARG cc_start: 0.6357 (ttp-170) cc_final: 0.6153 (mtp180) REVERT: X 93 LEU cc_start: 0.7121 (tp) cc_final: 0.6716 (tt) REVERT: Y 85 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6533 (ttp80) REVERT: a 28 ARG cc_start: 0.6112 (ptt180) cc_final: 0.5269 (ptm160) REVERT: a 66 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7841 (mtmm) REVERT: b 76 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6097 (pp) REVERT: b 147 GLN cc_start: 0.7800 (tp40) cc_final: 0.7497 (tp40) REVERT: b 186 ARG cc_start: 0.5675 (ptm160) cc_final: 0.4901 (tpm170) outliers start: 264 outliers final: 230 residues processed: 1431 average time/residue: 0.5776 time to fit residues: 1319.2323 Evaluate side-chains 1468 residues out of total 4612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1225 time to evaluate : 4.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 VAL 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 235 ILE Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 151 ASP 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 42 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 205 VAL 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 229 PHE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 37 ILE 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 220 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 MET 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 38 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 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 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 14 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 59 LEU 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 122 SER Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 63 LEU 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 163 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 151 ASP 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 42 VAL 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 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 205 VAL 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 229 PHE Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 174 ARG Chi-restraints excluded: chain U residue 37 ILE 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 U residue 220 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 8 PHE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain V residue 169 SER 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 38 SER Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU 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 57 THR 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 192 ASP Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 85 ARG Chi-restraints excluded: chain Y residue 184 ASP 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 102 CYS Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 133 ASP 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 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 342 optimal weight: 3.9990 chunk 459 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 397 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 119 optimal weight: 0.9990 chunk 432 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 443 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN ** O 24 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** ** T 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.193090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.187103 restraints weight = 73045.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.188647 restraints weight = 43964.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.189670 restraints weight = 28694.013| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 44174 Z= 0.247 Angle : 0.738 15.571 59622 Z= 0.375 Chirality : 0.047 0.276 6732 Planarity : 0.005 0.099 7614 Dihedral : 8.572 125.973 6264 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 5.64 % Allowed : 27.67 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.11), residues: 5432 helix: -0.23 (0.11), residues: 1914 sheet: -1.30 (0.14), residues: 1270 loop : -1.23 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 107 HIS 0.012 0.001 HIS V 66 PHE 0.047 0.002 PHE B 172 TYR 0.031 0.002 TYR Q 136 ARG 0.011 0.001 ARG L 120 =============================================================================== Job complete usr+sys time: 17887.73 seconds wall clock time: 316 minutes 45.03 seconds (19005.03 seconds total)