Starting phenix.real_space_refine on Fri Mar 6 22:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d74_30601/03_2026/7d74_30601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d74_30601/03_2026/7d74_30601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d74_30601/03_2026/7d74_30601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d74_30601/03_2026/7d74_30601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d74_30601/03_2026/7d74_30601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d74_30601/03_2026/7d74_30601.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 220 5.16 5 C 22400 2.51 5 N 6202 2.21 5 O 6495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 414 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35353 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2785 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "F" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2782 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 22, 'TRANS': 336} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "H" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "I" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "J" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "K" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "L" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.28, per 1000 atoms: 0.23 Number of scatterers: 35353 At special positions: 0 Unit cell: (138.864, 195.672, 190.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 36 15.00 O 6495 8.00 N 6202 7.00 C 22400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 289 " - pdb=" SG CYS H 306 " distance=2.23 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8270 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 86 sheets defined 27.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.991A pdb=" N GLY A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.858A pdb=" N LEU A 150 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 removed outlier: 4.151A pdb=" N LEU A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 265 removed outlier: 4.040A pdb=" N TYR A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 37 through 46 Processing helix chain 'D' and resid 62 through 77 Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.991A pdb=" N GLY D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 122 through 134 Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.857A pdb=" N LEU D 150 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 removed outlier: 4.151A pdb=" N LEU D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 removed outlier: 4.040A pdb=" N TYR D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 62 through 77 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.991A pdb=" N GLY B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.858A pdb=" N LEU B 150 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 removed outlier: 4.151A pdb=" N LEU B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 265 removed outlier: 4.040A pdb=" N TYR B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 62 through 77 Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.991A pdb=" N GLY C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 122 through 134 Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.857A pdb=" N LEU C 150 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 removed outlier: 4.152A pdb=" N LEU C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 265 removed outlier: 4.041A pdb=" N TYR C 256 " --> pdb=" O GLY C 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 22 through 26 removed outlier: 3.622A pdb=" N VAL E 26 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 45 Processing helix chain 'E' and resid 57 through 72 Processing helix chain 'E' and resid 87 through 93 Processing helix chain 'E' and resid 93 through 99 Processing helix chain 'E' and resid 116 through 128 Processing helix chain 'E' and resid 179 through 186 removed outlier: 3.539A pdb=" N LEU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.700A pdb=" N GLU E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Proline residue: E 199 - end of helix Processing helix chain 'E' and resid 221 through 240 Processing helix chain 'F' and resid 14 through 19 Processing helix chain 'F' and resid 22 through 26 removed outlier: 3.812A pdb=" N VAL F 26 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 45 Processing helix chain 'F' and resid 57 through 72 Processing helix chain 'F' and resid 87 through 93 removed outlier: 3.505A pdb=" N ALA F 93 " --> pdb=" O PRO F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 140 through 144 removed outlier: 3.735A pdb=" N LYS F 143 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR F 144 " --> pdb=" O PRO F 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 140 through 144' Processing helix chain 'F' and resid 179 through 186 Processing helix chain 'F' and resid 196 through 205 Processing helix chain 'F' and resid 221 through 240 Processing helix chain 'G' and resid 14 through 19 Processing helix chain 'G' and resid 22 through 26 removed outlier: 3.694A pdb=" N VAL G 26 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 45 Processing helix chain 'G' and resid 57 through 72 Processing helix chain 'G' and resid 87 through 93 removed outlier: 3.511A pdb=" N ALA G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 140 through 144 removed outlier: 3.602A pdb=" N LYS G 143 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 144 " --> pdb=" O PRO G 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 140 through 144' Processing helix chain 'G' and resid 179 through 186 removed outlier: 3.559A pdb=" N LEU G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 204 removed outlier: 3.723A pdb=" N GLU G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) Proline residue: G 199 - end of helix Processing helix chain 'G' and resid 221 through 238 Processing helix chain 'H' and resid 14 through 19 Processing helix chain 'H' and resid 22 through 26 removed outlier: 3.702A pdb=" N VAL H 26 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 45 Processing helix chain 'H' and resid 57 through 72 removed outlier: 3.568A pdb=" N GLY H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 93 removed outlier: 3.767A pdb=" N ALA H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 98 Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 179 through 186 removed outlier: 3.670A pdb=" N LEU H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 221 through 240 Processing helix chain 'I' and resid 14 through 19 Processing helix chain 'I' and resid 22 through 26 removed outlier: 3.834A pdb=" N VAL I 26 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 45 Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.548A pdb=" N GLY I 72 " --> pdb=" O GLU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 93 Processing helix chain 'I' and resid 93 through 98 removed outlier: 3.501A pdb=" N LEU I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 179 through 186 removed outlier: 3.615A pdb=" N LEU I 183 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 204 Processing helix chain 'I' and resid 221 through 238 Processing helix chain 'J' and resid 14 through 19 Processing helix chain 'J' and resid 22 through 26 removed outlier: 3.710A pdb=" N VAL J 26 " --> pdb=" O LYS J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 45 Processing helix chain 'J' and resid 57 through 72 removed outlier: 4.013A pdb=" N GLY J 72 " --> pdb=" O GLU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 93 removed outlier: 3.549A pdb=" N ALA J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 98 Processing helix chain 'J' and resid 116 through 128 Processing helix chain 'J' and resid 140 through 144 removed outlier: 3.681A pdb=" N LYS J 143 " --> pdb=" O GLU J 140 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR J 144 " --> pdb=" O PRO J 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 140 through 144' Processing helix chain 'J' and resid 179 through 186 removed outlier: 3.536A pdb=" N LEU J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 205 removed outlier: 3.813A pdb=" N LYS J 203 " --> pdb=" O PRO J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 Processing helix chain 'K' and resid 14 through 19 Processing helix chain 'K' and resid 22 through 26 removed outlier: 3.631A pdb=" N VAL K 26 " --> pdb=" O LYS K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 45 Processing helix chain 'K' and resid 57 through 72 removed outlier: 3.729A pdb=" N GLY K 72 " --> pdb=" O GLU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 93 removed outlier: 3.682A pdb=" N ALA K 93 " --> pdb=" O PRO K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 98 Processing helix chain 'K' and resid 116 through 128 Processing helix chain 'K' and resid 140 through 144 removed outlier: 3.815A pdb=" N LYS K 143 " --> pdb=" O GLU K 140 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR K 144 " --> pdb=" O PRO K 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 140 through 144' Processing helix chain 'K' and resid 179 through 186 removed outlier: 3.790A pdb=" N LEU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 204 Processing helix chain 'K' and resid 221 through 240 Processing helix chain 'L' and resid 14 through 19 Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.653A pdb=" N VAL L 26 " --> pdb=" O LYS L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 45 Processing helix chain 'L' and resid 57 through 72 removed outlier: 3.577A pdb=" N GLY L 72 " --> pdb=" O GLU L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 93 removed outlier: 3.512A pdb=" N ALA L 93 " --> pdb=" O PRO L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 98 Processing helix chain 'L' and resid 116 through 128 Processing helix chain 'L' and resid 179 through 186 removed outlier: 3.535A pdb=" N LEU L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 204 Processing helix chain 'L' and resid 221 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 8.444A pdb=" N ARG A 81 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 53 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 83 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU A 55 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU A 2 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N LEU A 54 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 4 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE A 56 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 6 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY A 182 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU A 140 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 183 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 138 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.594A pdb=" N VAL A 34 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 158 removed outlier: 6.765A pdb=" N CYS A 154 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 167 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 156 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 163 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 283 removed outlier: 6.694A pdb=" N TRP A 282 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 300 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG A 318 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 352 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.575A pdb=" N SER A 306 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 323 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 340 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 386 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 403 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 294 through 295 removed outlier: 6.799A pdb=" N LYS A 294 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A 312 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR A 329 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 346 " --> pdb=" O ILE A 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA9, first strand: chain 'D' and resid 80 through 84 removed outlier: 8.445A pdb=" N ARG D 81 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 53 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU D 83 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D 55 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU D 2 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N LEU D 54 " --> pdb=" O LEU D 2 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA D 4 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE D 56 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE D 6 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY D 182 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU D 140 " --> pdb=" O CYS D 181 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE D 183 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU D 138 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.593A pdb=" N VAL D 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AB3, first strand: chain 'D' and resid 154 through 158 removed outlier: 6.765A pdb=" N CYS D 154 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR D 167 " --> pdb=" O CYS D 154 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL D 156 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 163 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.694A pdb=" N TRP D 282 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 300 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG D 318 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG D 352 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 287 through 289 removed outlier: 6.575A pdb=" N SER D 306 " --> pdb=" O VAL D 324 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE D 323 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 340 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 386 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 403 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 294 through 295 removed outlier: 6.799A pdb=" N LYS D 294 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR D 312 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR D 329 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR D 346 " --> pdb=" O ILE D 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 375 through 376 Processing sheet with id=AB8, first strand: chain 'B' and resid 80 through 84 removed outlier: 8.444A pdb=" N ARG B 81 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 53 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 83 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 55 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 2 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N LEU B 54 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA B 4 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE B 56 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 6 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY B 182 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 140 " --> pdb=" O CYS B 181 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE B 183 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU B 138 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.593A pdb=" N VAL B 34 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AC2, first strand: chain 'B' and resid 154 through 158 removed outlier: 6.765A pdb=" N CYS B 154 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR B 167 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 156 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 163 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 282 through 283 removed outlier: 6.694A pdb=" N TRP B 282 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 300 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG B 318 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG B 352 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.575A pdb=" N SER B 306 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 323 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 340 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE B 386 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 403 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 294 through 295 removed outlier: 6.799A pdb=" N LYS B 294 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR B 312 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR B 329 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 346 " --> pdb=" O ILE B 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 375 through 376 Processing sheet with id=AC7, first strand: chain 'C' and resid 80 through 84 removed outlier: 8.444A pdb=" N ARG C 81 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 53 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C 83 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU C 55 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU C 2 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N LEU C 54 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA C 4 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE C 56 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE C 6 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY C 182 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 140 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE C 183 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU C 138 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.593A pdb=" N VAL C 34 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AD1, first strand: chain 'C' and resid 154 through 158 removed outlier: 6.764A pdb=" N CYS C 154 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR C 167 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 156 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 163 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 282 through 283 removed outlier: 6.694A pdb=" N TRP C 282 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 300 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG C 318 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 352 " --> pdb=" O ILE C 399 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 287 through 289 removed outlier: 6.574A pdb=" N SER C 306 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 323 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 340 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 386 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 403 " --> pdb=" O ILE C 419 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 294 through 295 removed outlier: 6.798A pdb=" N LYS C 294 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR C 312 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR C 329 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR C 346 " --> pdb=" O ILE C 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 375 through 376 Processing sheet with id=AD6, first strand: chain 'E' and resid 74 through 79 removed outlier: 3.705A pdb=" N SER E 76 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA E 3 " --> pdb=" O HIS E 48 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLY E 174 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA E 173 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR E 136 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N MET E 175 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 111 through 113 Processing sheet with id=AD8, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.713A pdb=" N LEU E 255 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER E 273 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR E 290 " --> pdb=" O VAL E 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 261 through 262 removed outlier: 6.337A pdb=" N ARG E 261 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL E 279 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG E 296 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG E 313 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE E 331 " --> pdb=" O ILE E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 285 through 287 removed outlier: 6.401A pdb=" N ARG E 319 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 342 through 343 removed outlier: 6.426A pdb=" N SER E 342 " --> pdb=" O ILE E 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 74 through 79 removed outlier: 6.279A pdb=" N VAL F 49 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER F 78 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU F 51 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F 3 " --> pdb=" O HIS F 48 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY F 174 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 134 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET F 175 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER F 132 " --> pdb=" O MET F 175 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 111 through 113 Processing sheet with id=AE5, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AE6, first strand: chain 'F' and resid 254 through 256 removed outlier: 6.489A pdb=" N SER F 273 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 261 through 262 removed outlier: 6.310A pdb=" N ARG F 261 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL F 279 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG F 296 " --> pdb=" O VAL F 314 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG F 313 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 331 " --> pdb=" O ILE F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 285 through 287 removed outlier: 6.300A pdb=" N CYS F 285 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG F 319 " --> pdb=" O LEU F 338 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 342 through 343 removed outlier: 6.498A pdb=" N SER F 342 " --> pdb=" O ILE F 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'G' and resid 74 through 76 removed outlier: 6.338A pdb=" N ALA G 3 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU G 134 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N MET G 175 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER G 132 " --> pdb=" O MET G 175 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 111 through 113 Processing sheet with id=AF3, first strand: chain 'G' and resid 254 through 256 removed outlier: 6.653A pdb=" N LEU G 255 " --> pdb=" O LEU G 274 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER G 273 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 261 through 262 removed outlier: 6.452A pdb=" N ARG G 261 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL G 279 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG G 296 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG G 313 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE G 331 " --> pdb=" O ILE G 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.486A pdb=" N ARG G 319 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 342 through 343 removed outlier: 6.495A pdb=" N SER G 342 " --> pdb=" O ILE G 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'H' and resid 74 through 79 removed outlier: 3.761A pdb=" N ALA H 3 " --> pdb=" O HIS H 48 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLY H 174 " --> pdb=" O ASN H 108 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA H 173 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR H 136 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET H 175 " --> pdb=" O LEU H 134 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 111 through 113 Processing sheet with id=AF9, first strand: chain 'H' and resid 147 through 149 removed outlier: 3.632A pdb=" N VAL H 148 " --> pdb=" O ARG H 158 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG H 158 " --> pdb=" O VAL H 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'H' and resid 254 through 256 removed outlier: 6.708A pdb=" N LEU H 255 " --> pdb=" O LEU H 274 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER H 273 " --> pdb=" O VAL H 291 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 261 through 262 removed outlier: 6.393A pdb=" N ARG H 261 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL H 279 " --> pdb=" O ILE H 297 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG H 296 " --> pdb=" O VAL H 314 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG H 313 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE H 331 " --> pdb=" O ILE H 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'H' and resid 285 through 287 removed outlier: 6.447A pdb=" N ARG H 319 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 342 through 343 removed outlier: 6.376A pdb=" N SER H 342 " --> pdb=" O ILE H 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'I' and resid 74 through 79 removed outlier: 6.498A pdb=" N VAL I 49 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER I 78 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU I 51 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA I 3 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA I 52 " --> pdb=" O ALA I 3 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE I 5 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLY I 174 " --> pdb=" O ASN I 108 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU I 134 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET I 175 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER I 132 " --> pdb=" O MET I 175 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 111 through 113 Processing sheet with id=AG7, first strand: chain 'I' and resid 146 through 149 removed outlier: 3.667A pdb=" N VAL I 148 " --> pdb=" O ARG I 158 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG I 158 " --> pdb=" O VAL I 148 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 254 through 256 removed outlier: 6.607A pdb=" N LEU I 255 " --> pdb=" O LEU I 274 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER I 273 " --> pdb=" O VAL I 291 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE I 307 " --> pdb=" O THR I 324 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 261 through 262 removed outlier: 6.314A pdb=" N ARG I 261 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL I 279 " --> pdb=" O ILE I 297 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG I 296 " --> pdb=" O VAL I 314 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG I 313 " --> pdb=" O VAL I 332 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE I 331 " --> pdb=" O ILE I 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'I' and resid 285 through 287 removed outlier: 6.490A pdb=" N ARG I 319 " --> pdb=" O LEU I 338 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 342 through 343 removed outlier: 6.625A pdb=" N SER I 342 " --> pdb=" O ILE I 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'J' and resid 74 through 79 removed outlier: 6.261A pdb=" N VAL J 49 " --> pdb=" O SER J 76 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER J 78 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU J 51 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ALA J 3 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA J 52 " --> pdb=" O ALA J 3 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE J 5 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY J 174 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU J 134 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N MET J 175 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N SER J 132 " --> pdb=" O MET J 175 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 111 through 113 Processing sheet with id=AH5, first strand: chain 'J' and resid 146 through 147 Processing sheet with id=AH6, first strand: chain 'J' and resid 254 through 256 removed outlier: 6.787A pdb=" N LEU J 255 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER J 273 " --> pdb=" O VAL J 291 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR J 290 " --> pdb=" O VAL J 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'J' and resid 261 through 262 removed outlier: 6.423A pdb=" N ARG J 261 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL J 279 " --> pdb=" O ILE J 297 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG J 296 " --> pdb=" O VAL J 314 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG J 313 " --> pdb=" O VAL J 332 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE J 331 " --> pdb=" O ILE J 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'J' and resid 285 through 287 removed outlier: 6.392A pdb=" N ARG J 319 " --> pdb=" O LEU J 338 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 342 through 343 removed outlier: 6.558A pdb=" N SER J 342 " --> pdb=" O ILE J 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'K' and resid 74 through 79 removed outlier: 6.073A pdb=" N ALA K 3 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ALA K 52 " --> pdb=" O ALA K 3 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE K 5 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY K 174 " --> pdb=" O ASN K 108 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU K 134 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET K 175 " --> pdb=" O SER K 132 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER K 132 " --> pdb=" O MET K 175 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 111 through 113 Processing sheet with id=AI3, first strand: chain 'K' and resid 146 through 147 Processing sheet with id=AI4, first strand: chain 'K' and resid 254 through 256 removed outlier: 6.697A pdb=" N LEU K 255 " --> pdb=" O LEU K 274 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER K 273 " --> pdb=" O VAL K 291 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE K 307 " --> pdb=" O THR K 324 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 261 through 262 removed outlier: 6.327A pdb=" N ARG K 261 " --> pdb=" O VAL K 280 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL K 279 " --> pdb=" O ILE K 297 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG K 296 " --> pdb=" O VAL K 314 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG K 313 " --> pdb=" O VAL K 332 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE K 331 " --> pdb=" O ILE K 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'K' and resid 285 through 287 removed outlier: 6.328A pdb=" N CYS K 285 " --> pdb=" O LEU K 303 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG K 319 " --> pdb=" O LEU K 338 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 342 through 343 removed outlier: 6.338A pdb=" N SER K 342 " --> pdb=" O ILE K 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'L' and resid 74 through 79 removed outlier: 3.749A pdb=" N ALA L 3 " --> pdb=" O HIS L 48 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY L 174 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS L 170 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 148 " --> pdb=" O ARG L 158 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG L 158 " --> pdb=" O VAL L 148 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 74 through 79 removed outlier: 3.749A pdb=" N ALA L 3 " --> pdb=" O HIS L 48 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY L 174 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA L 173 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR L 136 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N MET L 175 " --> pdb=" O LEU L 134 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 111 through 113 Processing sheet with id=AJ2, first strand: chain 'L' and resid 254 through 256 removed outlier: 6.903A pdb=" N LEU L 255 " --> pdb=" O LEU L 274 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER L 273 " --> pdb=" O VAL L 291 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 261 through 262 removed outlier: 6.517A pdb=" N ARG L 261 " --> pdb=" O VAL L 280 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL L 279 " --> pdb=" O ILE L 297 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG L 296 " --> pdb=" O VAL L 314 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG L 313 " --> pdb=" O VAL L 332 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE L 331 " --> pdb=" O ILE L 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'L' and resid 285 through 287 removed outlier: 6.455A pdb=" N ARG L 319 " --> pdb=" O LEU L 338 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'L' and resid 342 through 343 removed outlier: 6.531A pdb=" N SER L 342 " --> pdb=" O ILE L 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 1069 hydrogen bonds defined for protein. 3027 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: 8.96 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8783 1.33 - 1.47: 10554 1.47 - 1.60: 16415 1.60 - 1.74: 53 1.74 - 1.88: 335 Bond restraints: 36140 Sorted by residual: bond pdb=" O2G GTP G 401 " pdb=" PG GTP G 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O2G GTP H 401 " pdb=" PG GTP H 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O2G GTP F 401 " pdb=" PG GTP F 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" O2G GTP K 401 " pdb=" PG GTP K 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" O2G GTP E 401 " pdb=" PG GTP E 401 " ideal model delta sigma weight residual 1.510 1.620 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 36135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 48411 4.74 - 9.47: 642 9.47 - 14.21: 79 14.21 - 18.94: 3 18.94 - 23.68: 8 Bond angle restraints: 49143 Sorted by residual: angle pdb=" N GLY F 9 " pdb=" CA GLY F 9 " pdb=" C GLY F 9 " ideal model delta sigma weight residual 110.56 127.47 -16.91 1.66e+00 3.63e-01 1.04e+02 angle pdb=" N2 GTP F 401 " pdb=" C2 GTP F 401 " pdb=" N3 GTP F 401 " ideal model delta sigma weight residual 120.00 96.32 23.68 3.00e+00 1.11e-01 6.23e+01 angle pdb=" N2 GTP E 401 " pdb=" C2 GTP E 401 " pdb=" N3 GTP E 401 " ideal model delta sigma weight residual 120.00 96.35 23.65 3.00e+00 1.11e-01 6.22e+01 angle pdb=" N2 GTP I 401 " pdb=" C2 GTP I 401 " pdb=" N3 GTP I 401 " ideal model delta sigma weight residual 120.00 96.36 23.64 3.00e+00 1.11e-01 6.21e+01 angle pdb=" N2 GTP J 401 " pdb=" C2 GTP J 401 " pdb=" N3 GTP J 401 " ideal model delta sigma weight residual 120.00 96.37 23.63 3.00e+00 1.11e-01 6.20e+01 ... (remaining 49138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 20636 35.35 - 70.71: 1084 70.71 - 106.06: 70 106.06 - 141.41: 8 141.41 - 176.77: 12 Dihedral angle restraints: 21810 sinusoidal: 8962 harmonic: 12848 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -72.18 176.77 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -72.17 176.77 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -72.15 176.74 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 21807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4922 0.114 - 0.228: 522 0.228 - 0.341: 87 0.341 - 0.455: 17 0.455 - 0.569: 2 Chirality restraints: 5550 Sorted by residual: chirality pdb=" CG LEU F 84 " pdb=" CB LEU F 84 " pdb=" CD1 LEU F 84 " pdb=" CD2 LEU F 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" CB VAL H 46 " pdb=" CA VAL H 46 " pdb=" CG1 VAL H 46 " pdb=" CG2 VAL H 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CB ILE F 200 " pdb=" CA ILE F 200 " pdb=" CG1 ILE F 200 " pdb=" CG2 ILE F 200 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 5547 not shown) Planarity restraints: 6322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 401 " 0.020 2.00e-02 2.50e+03 3.89e-02 4.54e+01 pdb=" C2 GTP L 401 " 0.113 2.00e-02 2.50e+03 pdb=" C4 GTP L 401 " 0.002 2.00e-02 2.50e+03 pdb=" C5 GTP L 401 " -0.004 2.00e-02 2.50e+03 pdb=" C6 GTP L 401 " -0.001 2.00e-02 2.50e+03 pdb=" C8 GTP L 401 " 0.000 2.00e-02 2.50e+03 pdb=" N1 GTP L 401 " -0.019 2.00e-02 2.50e+03 pdb=" N2 GTP L 401 " -0.037 2.00e-02 2.50e+03 pdb=" N3 GTP L 401 " -0.056 2.00e-02 2.50e+03 pdb=" N7 GTP L 401 " -0.003 2.00e-02 2.50e+03 pdb=" N9 GTP L 401 " -0.011 2.00e-02 2.50e+03 pdb=" O6 GTP L 401 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP F 401 " 0.020 2.00e-02 2.50e+03 3.89e-02 4.54e+01 pdb=" C2 GTP F 401 " 0.113 2.00e-02 2.50e+03 pdb=" C4 GTP F 401 " 0.002 2.00e-02 2.50e+03 pdb=" C5 GTP F 401 " -0.004 2.00e-02 2.50e+03 pdb=" C6 GTP F 401 " -0.001 2.00e-02 2.50e+03 pdb=" C8 GTP F 401 " 0.001 2.00e-02 2.50e+03 pdb=" N1 GTP F 401 " -0.018 2.00e-02 2.50e+03 pdb=" N2 GTP F 401 " -0.037 2.00e-02 2.50e+03 pdb=" N3 GTP F 401 " -0.057 2.00e-02 2.50e+03 pdb=" N7 GTP F 401 " -0.003 2.00e-02 2.50e+03 pdb=" N9 GTP F 401 " -0.011 2.00e-02 2.50e+03 pdb=" O6 GTP F 401 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP E 401 " -0.020 2.00e-02 2.50e+03 3.89e-02 4.54e+01 pdb=" C2 GTP E 401 " -0.113 2.00e-02 2.50e+03 pdb=" C4 GTP E 401 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GTP E 401 " 0.004 2.00e-02 2.50e+03 pdb=" C6 GTP E 401 " 0.001 2.00e-02 2.50e+03 pdb=" C8 GTP E 401 " -0.000 2.00e-02 2.50e+03 pdb=" N1 GTP E 401 " 0.019 2.00e-02 2.50e+03 pdb=" N2 GTP E 401 " 0.037 2.00e-02 2.50e+03 pdb=" N3 GTP E 401 " 0.057 2.00e-02 2.50e+03 pdb=" N7 GTP E 401 " 0.003 2.00e-02 2.50e+03 pdb=" N9 GTP E 401 " 0.011 2.00e-02 2.50e+03 pdb=" O6 GTP E 401 " 0.003 2.00e-02 2.50e+03 ... (remaining 6319 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 170 2.52 - 3.11: 22731 3.11 - 3.71: 55498 3.71 - 4.30: 80242 4.30 - 4.90: 134809 Nonbonded interactions: 293450 Sorted by model distance: nonbonded pdb=" NH1 ARG D 259 " pdb=" OE1 GLU D 321 " model vdw 1.922 3.120 nonbonded pdb=" CG HIS I 346 " pdb=" CE2 TYR J 10 " model vdw 2.132 3.560 nonbonded pdb=" CA GLY E 8 " pdb=" N2 GTP E 401 " model vdw 2.158 2.816 nonbonded pdb=" OE2 GLU L 321 " pdb=" CE1 TYR L 337 " model vdw 2.201 3.340 nonbonded pdb=" N GLY F 9 " pdb=" O2' GTP F 401 " model vdw 2.231 3.120 ... (remaining 293445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 6 or resid 8 through 401)) selection = (chain 'F' and (resid 1 through 6 or resid 8 through 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 through 401)) selection = (chain 'G' and (resid 1 through 161 or (resid 162 and (name N or name CA or name \ C or name O or name CB )) or resid 163 through 401)) selection = (chain 'H' and (resid 1 through 6 or resid 8 through 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 through 401)) selection = (chain 'I' and (resid 1 through 6 or resid 8 through 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 through 401)) selection = (chain 'J' and (resid 1 through 6 or resid 8 through 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 through 401)) selection = (chain 'K' and (resid 1 through 6 or resid 8 through 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 through 401)) selection = (chain 'L' and (resid 1 through 6 or resid 8 through 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 through 401)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 35.980 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 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 : 0.017 0.813 36160 Z= 1.506 Angle : 1.386 24.206 49145 Z= 0.730 Chirality : 0.079 0.569 5550 Planarity : 0.010 0.080 6322 Dihedral : 19.734 176.768 13537 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.83 % Favored : 94.81 % Rotamer: Outliers : 8.87 % Allowed : 17.88 % Favored : 73.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.11), residues: 4469 helix: -2.85 (0.12), residues: 1015 sheet: -0.97 (0.19), residues: 668 loop : -1.32 (0.10), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 158 TYR 0.038 0.003 TYR E 144 PHE 0.066 0.004 PHE K 166 TRP 0.018 0.003 TRP F 302 HIS 0.022 0.003 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00944 (36140) covalent geometry : angle 1.38172 (49143) SS BOND : bond 0.19475 ( 1) SS BOND : angle 17.25686 ( 2) hydrogen bonds : bond 0.16703 ( 1052) hydrogen bonds : angle 7.86195 ( 3027) Misc. bond : bond 0.63110 ( 19) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 350 poor density : 634 time to evaluate : 1.315 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping revert: symmetry clash REVERT: A 282 TRP cc_start: 0.6157 (m-90) cc_final: 0.5773 (m-90) REVERT: A 294 LYS cc_start: 0.7238 (ptpt) cc_final: 0.6682 (mmmt) REVERT: A 329 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7770 (m) REVERT: D 13 LYS cc_start: 0.8076 (mppt) cc_final: 0.7850 (mmmt) REVERT: D 51 GLN cc_start: 0.7062 (tt0) cc_final: 0.6519 (tt0) REVERT: D 264 ARG cc_start: 0.7412 (tpt170) cc_final: 0.7188 (tpt170) REVERT: D 295 VAL cc_start: 0.8726 (t) cc_final: 0.8491 (m) REVERT: D 329 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7207 (p) REVERT: D 373 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7334 (p) REVERT: D 377 ASP cc_start: 0.5463 (m-30) cc_final: 0.5031 (m-30) REVERT: B 66 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7657 (m) REVERT: B 133 GLN cc_start: 0.5630 (mm110) cc_final: 0.5305 (pt0) REVERT: B 162 HIS cc_start: 0.6322 (m-70) cc_final: 0.6017 (m-70) REVERT: B 170 LYS cc_start: 0.7608 (mttt) cc_final: 0.7322 (mmtm) REVERT: B 240 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 272 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7382 (mtt180) REVERT: B 321 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7038 (mm-30) REVERT: B 364 ASP cc_start: 0.6955 (t0) cc_final: 0.6653 (t70) REVERT: C 166 HIS cc_start: 0.6864 (t70) cc_final: 0.6569 (t70) REVERT: C 173 THR cc_start: 0.6022 (OUTLIER) cc_final: 0.5822 (t) REVERT: C 309 LYS cc_start: 0.7779 (pttt) cc_final: 0.7515 (ptmt) REVERT: C 312 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7654 (m) REVERT: C 329 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7598 (m) REVERT: C 354 GLU cc_start: 0.7008 (tt0) cc_final: 0.6719 (tt0) REVERT: C 361 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7423 (t0) REVERT: C 390 ARG cc_start: 0.7427 (mtp85) cc_final: 0.7141 (mmt180) REVERT: E 25 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.5056 (mp) REVERT: E 81 GLU cc_start: 0.1756 (OUTLIER) cc_final: 0.1190 (tm-30) REVERT: E 120 MET cc_start: 0.1742 (ttt) cc_final: 0.1077 (mtp) REVERT: E 126 HIS cc_start: 0.3458 (OUTLIER) cc_final: 0.3033 (m170) REVERT: E 144 TYR cc_start: 0.0947 (OUTLIER) cc_final: 0.0510 (m-10) REVERT: E 355 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6360 (mt-10) REVERT: E 357 ARG cc_start: 0.6450 (ptt-90) cc_final: 0.6244 (ptt180) REVERT: F 19 LEU cc_start: 0.6785 (mt) cc_final: 0.6568 (mt) REVERT: F 82 GLU cc_start: 0.2249 (OUTLIER) cc_final: 0.1995 (pm20) REVERT: F 233 LEU cc_start: 0.7858 (mt) cc_final: 0.7405 (mt) REVERT: F 265 ASN cc_start: 0.6573 (t0) cc_final: 0.6024 (t0) REVERT: F 323 VAL cc_start: 0.8975 (m) cc_final: 0.8673 (t) REVERT: G 33 ILE cc_start: 0.5022 (OUTLIER) cc_final: 0.4554 (mp) REVERT: G 201 MET cc_start: 0.2301 (mtp) cc_final: 0.1945 (mtt) REVERT: G 311 ARG cc_start: 0.5791 (mtm110) cc_final: 0.5533 (mtm180) REVERT: G 335 GLU cc_start: 0.3973 (mt-10) cc_final: 0.3728 (mt-10) REVERT: H 1 MET cc_start: 0.2273 (ttp) cc_final: 0.1045 (ptm) REVERT: H 223 LYS cc_start: 0.7228 (pttp) cc_final: 0.6948 (pttm) REVERT: H 329 ASP cc_start: 0.6696 (t0) cc_final: 0.6468 (t0) REVERT: I 34 LEU cc_start: 0.6526 (tp) cc_final: 0.6239 (tp) REVERT: I 102 ASP cc_start: 0.0330 (OUTLIER) cc_final: -0.0035 (p0) REVERT: I 134 LEU cc_start: 0.1881 (OUTLIER) cc_final: 0.1463 (tt) REVERT: I 229 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5919 (ttp) REVERT: I 232 PHE cc_start: 0.6840 (t80) cc_final: 0.6571 (t80) REVERT: I 238 GLN cc_start: 0.4761 (OUTLIER) cc_final: 0.4522 (mp10) REVERT: I 322 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6888 (m110) REVERT: J 217 MET cc_start: 0.1189 (tpp) cc_final: 0.0932 (tpp) REVERT: J 227 THR cc_start: 0.4825 (OUTLIER) cc_final: 0.4421 (t) REVERT: J 244 LEU cc_start: 0.4410 (OUTLIER) cc_final: 0.4098 (mt) REVERT: K 39 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.5015 (mt-10) REVERT: K 82 GLU cc_start: 0.3314 (OUTLIER) cc_final: 0.2728 (tm-30) REVERT: K 189 GLN cc_start: 0.3809 (OUTLIER) cc_final: 0.2648 (mp-120) REVERT: K 229 MET cc_start: 0.6963 (tmm) cc_final: 0.6611 (ttp) REVERT: K 282 ASP cc_start: 0.5958 (t0) cc_final: 0.5718 (t0) REVERT: L 32 PRO cc_start: 0.4960 (Cg_exo) cc_final: 0.4620 (Cg_endo) REVERT: L 60 LEU cc_start: 0.4340 (tp) cc_final: 0.4056 (tp) REVERT: L 107 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4551 (tp) REVERT: L 157 HIS cc_start: 0.1853 (OUTLIER) cc_final: 0.0799 (t-90) REVERT: L 236 LEU cc_start: 0.4675 (OUTLIER) cc_final: 0.3622 (tt) REVERT: L 286 ILE cc_start: 0.7310 (mm) cc_final: 0.6998 (mt) REVERT: L 296 ARG cc_start: 0.4304 (ttt90) cc_final: 0.4088 (ttm-80) REVERT: L 346 HIS cc_start: 0.6631 (m90) cc_final: 0.6388 (m170) outliers start: 350 outliers final: 109 residues processed: 923 average time/residue: 0.2304 time to fit residues: 335.2392 Evaluate side-chains 544 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 407 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 144 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 306 CYS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 149 CYS Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 175 MET Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 303 LEU Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 342 SER Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 238 GLN Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 322 ASN Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 266 CYS Chi-restraints excluded: chain J residue 306 CYS Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 246 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 0.0050 chunk 424 optimal weight: 6.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 40 HIS A 74 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN A 304 ASN A 401 ASN D 12 GLN D 40 HIS D 135 HIS D 158 ASN D 166 HIS D 326 HIS D 401 ASN B 40 HIS B 158 ASN B 276 HIS B 401 ASN C 40 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 401 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS E 240 GLN E 271 ASN E 316 GLN ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 GLN G 48 HIS ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 GLN G 300 HIS G 316 GLN H 67 GLN H 79 HIS ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN H 264 GLN H 316 GLN H 339 ASN I 122 GLN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN I 157 HIS I 346 HIS ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 253 ASN K 69 GLN ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 GLN K 316 GLN L 37 GLN L 69 GLN ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN L 172 ASN L 271 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.225480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.206270 restraints weight = 42092.778| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 1.00 r_work: 0.4102 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4040 r_free = 0.4040 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36160 Z= 0.138 Angle : 0.660 15.636 49145 Z= 0.322 Chirality : 0.050 0.238 5550 Planarity : 0.007 0.203 6322 Dihedral : 12.496 175.646 5207 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 4.10 % Allowed : 19.82 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.11), residues: 4469 helix: -1.08 (0.14), residues: 1036 sheet: -0.94 (0.15), residues: 1104 loop : -0.98 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.000 ARG L 13 TYR 0.013 0.001 TYR H 176 PHE 0.020 0.002 PHE A 110 TRP 0.013 0.002 TRP C 350 HIS 0.011 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00311 (36140) covalent geometry : angle 0.65916 (49143) SS BOND : bond 0.00692 ( 1) SS BOND : angle 3.44583 ( 2) hydrogen bonds : bond 0.04077 ( 1052) hydrogen bonds : angle 5.82234 ( 3027) Misc. bond : bond 0.00429 ( 19) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 412 time to evaluate : 1.619 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 282 TRP cc_start: 0.6796 (m-90) cc_final: 0.6347 (m-90) REVERT: A 294 LYS cc_start: 0.7614 (ptpt) cc_final: 0.6788 (mmmt) REVERT: D 13 LYS cc_start: 0.7942 (mppt) cc_final: 0.7726 (mmmt) REVERT: D 192 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7587 (ttpp) REVERT: D 264 ARG cc_start: 0.7658 (tpt170) cc_final: 0.7349 (tpt170) REVERT: D 321 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7151 (mt-10) REVERT: D 377 ASP cc_start: 0.5720 (m-30) cc_final: 0.5220 (m-30) REVERT: B 78 LEU cc_start: 0.7151 (tp) cc_final: 0.6799 (mp) REVERT: B 158 ASN cc_start: 0.5856 (OUTLIER) cc_final: 0.5295 (p0) REVERT: B 170 LYS cc_start: 0.7688 (mttt) cc_final: 0.7476 (mmtm) REVERT: C 354 GLU cc_start: 0.7364 (tt0) cc_final: 0.7156 (tt0) REVERT: C 368 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6838 (ttm170) REVERT: C 390 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7416 (mmt180) REVERT: C 412 ARG cc_start: 0.7667 (ptt90) cc_final: 0.7380 (ptt180) REVERT: E 117 PHE cc_start: 0.1196 (m-80) cc_final: 0.0782 (m-80) REVERT: E 320 MET cc_start: 0.7483 (mtm) cc_final: 0.7110 (mtm) REVERT: E 355 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6320 (mt-10) REVERT: E 357 ARG cc_start: 0.6595 (ptt-90) cc_final: 0.6358 (ptt180) REVERT: F 82 GLU cc_start: 0.2899 (OUTLIER) cc_final: 0.2038 (pm20) REVERT: F 112 ILE cc_start: 0.6562 (mm) cc_final: 0.6019 (tt) REVERT: F 122 GLN cc_start: 0.3735 (mt0) cc_final: 0.3325 (mm-40) REVERT: F 229 MET cc_start: 0.7145 (tmm) cc_final: 0.6853 (ttp) REVERT: F 233 LEU cc_start: 0.7696 (mt) cc_final: 0.7386 (mt) REVERT: F 265 ASN cc_start: 0.6755 (t0) cc_final: 0.6218 (t0) REVERT: F 289 CYS cc_start: 0.8361 (m) cc_final: 0.8074 (m) REVERT: F 323 VAL cc_start: 0.9004 (m) cc_final: 0.8734 (t) REVERT: G 33 ILE cc_start: 0.5126 (OUTLIER) cc_final: 0.4746 (mp) REVERT: H 1 MET cc_start: 0.3095 (ttp) cc_final: 0.2241 (ptm) REVERT: H 56 MET cc_start: 0.3443 (tpp) cc_final: 0.3071 (tpt) REVERT: H 75 ILE cc_start: 0.4703 (OUTLIER) cc_final: 0.3896 (mp) REVERT: H 137 LYS cc_start: 0.3551 (OUTLIER) cc_final: 0.2737 (ttmt) REVERT: H 201 MET cc_start: 0.2805 (tpp) cc_final: 0.2120 (mtp) REVERT: I 134 LEU cc_start: 0.2109 (OUTLIER) cc_final: 0.1491 (tt) REVERT: I 229 MET cc_start: 0.6061 (tmm) cc_final: 0.5809 (ttp) REVERT: I 232 PHE cc_start: 0.6979 (t80) cc_final: 0.6583 (t80) REVERT: J 31 LYS cc_start: 0.3282 (mmtp) cc_final: 0.3001 (tptt) REVERT: K 1 MET cc_start: 0.3786 (OUTLIER) cc_final: 0.3448 (mtt) REVERT: K 120 MET cc_start: 0.4427 (tpp) cc_final: 0.3300 (tpp) REVERT: K 229 MET cc_start: 0.6940 (tmm) cc_final: 0.6630 (ttp) REVERT: K 282 ASP cc_start: 0.6468 (t0) cc_final: 0.6255 (t0) REVERT: K 322 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7297 (m-40) REVERT: L 7 VAL cc_start: 0.5750 (t) cc_final: 0.5486 (p) REVERT: L 32 PRO cc_start: 0.5394 (Cg_exo) cc_final: 0.5026 (Cg_endo) REVERT: L 50 ILE cc_start: 0.2910 (mp) cc_final: 0.2693 (tt) REVERT: L 80 GLU cc_start: 0.4057 (OUTLIER) cc_final: 0.3580 (tp30) REVERT: L 107 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.4651 (tp) REVERT: L 175 MET cc_start: 0.4284 (OUTLIER) cc_final: 0.3991 (mtm) REVERT: L 206 GLN cc_start: 0.2658 (mm-40) cc_final: 0.1987 (mm110) REVERT: L 236 LEU cc_start: 0.4675 (OUTLIER) cc_final: 0.3566 (tt) outliers start: 166 outliers final: 93 residues processed: 551 average time/residue: 0.2199 time to fit residues: 195.6699 Evaluate side-chains 458 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 353 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 175 MET Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 321 GLU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 342 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 77 MET Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 266 CYS Chi-restraints excluded: chain J residue 314 VAL Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 322 ASN Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 331 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 2 optimal weight: 0.9980 chunk 438 optimal weight: 0.5980 chunk 288 optimal weight: 2.9990 chunk 426 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 364 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 273 optimal weight: 2.9990 chunk 179 optimal weight: 0.0970 chunk 8 optimal weight: 5.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 201 ASN D 166 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 201 ASN C 12 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS E 37 GLN E 339 ASN F 48 HIS ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN G 169 ASN H 67 GLN H 264 GLN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 118 GLN ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.224856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.201551 restraints weight = 41921.096| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 1.14 r_work: 0.4017 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36160 Z= 0.112 Angle : 0.607 14.293 49145 Z= 0.293 Chirality : 0.049 0.168 5550 Planarity : 0.006 0.245 6322 Dihedral : 11.293 172.183 5091 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Rotamer: Outliers : 3.40 % Allowed : 21.25 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 4469 helix: -0.18 (0.15), residues: 1086 sheet: -0.88 (0.14), residues: 1187 loop : -0.86 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.000 ARG L 13 TYR 0.016 0.001 TYR F 10 PHE 0.024 0.001 PHE K 215 TRP 0.009 0.001 TRP D 245 HIS 0.009 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00254 (36140) covalent geometry : angle 0.60702 (49143) SS BOND : bond 0.00075 ( 1) SS BOND : angle 2.16566 ( 2) hydrogen bonds : bond 0.03621 ( 1052) hydrogen bonds : angle 5.37206 ( 3027) Misc. bond : bond 0.00340 ( 19) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 380 time to evaluate : 1.287 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 1 MET cc_start: 0.6921 (tmm) cc_final: 0.6662 (tpp) REVERT: A 282 TRP cc_start: 0.6948 (m-90) cc_final: 0.6673 (m100) REVERT: A 294 LYS cc_start: 0.7805 (ptpt) cc_final: 0.6902 (mmmt) REVERT: D 13 LYS cc_start: 0.8032 (mppt) cc_final: 0.7826 (mmmt) REVERT: D 192 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7526 (ttpp) REVERT: D 264 ARG cc_start: 0.7713 (tpt170) cc_final: 0.7475 (tpt170) REVERT: D 321 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7064 (mt-10) REVERT: D 377 ASP cc_start: 0.5783 (m-30) cc_final: 0.5574 (m-30) REVERT: B 51 GLN cc_start: 0.7030 (tm-30) cc_final: 0.6551 (tt0) REVERT: B 78 LEU cc_start: 0.7000 (tp) cc_final: 0.6701 (mp) REVERT: B 170 LYS cc_start: 0.7703 (mttt) cc_final: 0.7491 (mmtm) REVERT: C 368 ARG cc_start: 0.7203 (ttm170) cc_final: 0.6867 (ttm170) REVERT: C 390 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7454 (mmt180) REVERT: C 412 ARG cc_start: 0.7726 (ptt90) cc_final: 0.7419 (ptt180) REVERT: E 234 GLN cc_start: 0.2321 (OUTLIER) cc_final: 0.2047 (tt0) REVERT: E 240 GLN cc_start: 0.4411 (tt0) cc_final: 0.3443 (mm110) REVERT: E 314 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6317 (t) REVERT: E 320 MET cc_start: 0.7448 (mtm) cc_final: 0.7109 (mtm) REVERT: E 335 GLU cc_start: 0.3528 (mt-10) cc_final: 0.3011 (pt0) REVERT: E 355 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6442 (mt-10) REVERT: E 357 ARG cc_start: 0.6648 (ptt-90) cc_final: 0.6376 (ptt180) REVERT: F 82 GLU cc_start: 0.2587 (OUTLIER) cc_final: 0.1826 (pm20) REVERT: F 112 ILE cc_start: 0.6599 (mm) cc_final: 0.5960 (tt) REVERT: F 201 MET cc_start: 0.1786 (tmm) cc_final: 0.0560 (mtp) REVERT: F 233 LEU cc_start: 0.7639 (mt) cc_final: 0.7426 (mt) REVERT: F 265 ASN cc_start: 0.6660 (t0) cc_final: 0.6113 (t0) REVERT: F 323 VAL cc_start: 0.8996 (m) cc_final: 0.8767 (t) REVERT: G 33 ILE cc_start: 0.5154 (OUTLIER) cc_final: 0.4812 (mp) REVERT: H 21 THR cc_start: 0.7017 (p) cc_final: 0.6701 (t) REVERT: H 75 ILE cc_start: 0.4639 (OUTLIER) cc_final: 0.4079 (mp) REVERT: H 137 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.2829 (ttmt) REVERT: H 201 MET cc_start: 0.3000 (tpp) cc_final: 0.2070 (mtp) REVERT: I 79 HIS cc_start: 0.2474 (OUTLIER) cc_final: 0.1521 (m-70) REVERT: I 134 LEU cc_start: 0.2479 (OUTLIER) cc_final: 0.1861 (tt) REVERT: I 229 MET cc_start: 0.6148 (tmm) cc_final: 0.5825 (ttp) REVERT: I 232 PHE cc_start: 0.7111 (t80) cc_final: 0.6580 (t80) REVERT: I 236 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6746 (mp) REVERT: J 10 TYR cc_start: 0.4342 (OUTLIER) cc_final: 0.3899 (p90) REVERT: J 229 MET cc_start: 0.5434 (tmm) cc_final: 0.5146 (tmm) REVERT: J 278 VAL cc_start: 0.5285 (m) cc_final: 0.4881 (m) REVERT: J 293 ARG cc_start: 0.5649 (tmt170) cc_final: 0.4887 (ptp-170) REVERT: K 1 MET cc_start: 0.3563 (OUTLIER) cc_final: 0.3274 (mtt) REVERT: K 77 MET cc_start: 0.5224 (mpp) cc_final: 0.4995 (tpt) REVERT: K 229 MET cc_start: 0.7142 (tmm) cc_final: 0.6749 (ttp) REVERT: L 7 VAL cc_start: 0.6105 (t) cc_final: 0.5794 (p) REVERT: L 32 PRO cc_start: 0.5616 (Cg_exo) cc_final: 0.5310 (Cg_endo) REVERT: L 50 ILE cc_start: 0.3124 (mp) cc_final: 0.2418 (tt) REVERT: L 80 GLU cc_start: 0.3721 (OUTLIER) cc_final: 0.3440 (tp30) REVERT: L 107 LEU cc_start: 0.4946 (OUTLIER) cc_final: 0.4730 (tt) REVERT: L 231 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6366 (mt) REVERT: L 351 GLU cc_start: 0.4753 (mm-30) cc_final: 0.4410 (mm-30) REVERT: L 355 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6221 (mm-30) outliers start: 139 outliers final: 85 residues processed: 501 average time/residue: 0.2201 time to fit residues: 178.4367 Evaluate side-chains 455 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 356 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 122 GLN Chi-restraints excluded: chain G residue 175 MET Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 342 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 278 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 422 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 324 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 229 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 201 ASN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN G 234 GLN H 67 GLN H 253 ASN H 264 GLN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.223917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.194902 restraints weight = 41743.528| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.42 r_work: 0.3910 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36160 Z= 0.118 Angle : 0.607 14.122 49145 Z= 0.292 Chirality : 0.049 0.241 5550 Planarity : 0.005 0.121 6322 Dihedral : 11.040 171.381 5072 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 3.84 % Allowed : 21.59 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.12), residues: 4469 helix: 0.43 (0.16), residues: 1075 sheet: -0.66 (0.16), residues: 1034 loop : -0.60 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 13 TYR 0.013 0.001 TYR F 10 PHE 0.023 0.002 PHE F 225 TRP 0.011 0.001 TRP D 245 HIS 0.009 0.001 HIS K 124 Details of bonding type rmsd covalent geometry : bond 0.00273 (36140) covalent geometry : angle 0.60698 (49143) SS BOND : bond 0.00025 ( 1) SS BOND : angle 1.43089 ( 2) hydrogen bonds : bond 0.03424 ( 1052) hydrogen bonds : angle 5.15423 ( 3027) Misc. bond : bond 0.00281 ( 19) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 370 time to evaluate : 1.329 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 165 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7856 (mt) REVERT: A 282 TRP cc_start: 0.7241 (m-90) cc_final: 0.6860 (m100) REVERT: A 294 LYS cc_start: 0.7941 (ptpt) cc_final: 0.6977 (mmmt) REVERT: D 13 LYS cc_start: 0.8009 (mppt) cc_final: 0.7757 (mmmt) REVERT: D 192 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7525 (ttpp) REVERT: D 264 ARG cc_start: 0.7786 (tpt170) cc_final: 0.7576 (tpt170) REVERT: D 321 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7156 (mt-10) REVERT: B 51 GLN cc_start: 0.6922 (tm-30) cc_final: 0.6522 (tt0) REVERT: B 170 LYS cc_start: 0.7835 (mttt) cc_final: 0.7614 (mmtm) REVERT: B 349 ARG cc_start: 0.7893 (ptp90) cc_final: 0.7498 (ttp80) REVERT: C 368 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7016 (ttm170) REVERT: C 390 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7574 (mmt180) REVERT: C 412 ARG cc_start: 0.7853 (ptt90) cc_final: 0.7505 (ptt180) REVERT: E 10 TYR cc_start: 0.5481 (OUTLIER) cc_final: 0.2992 (p90) REVERT: E 48 HIS cc_start: 0.1829 (OUTLIER) cc_final: 0.1429 (p90) REVERT: E 120 MET cc_start: 0.2803 (ttt) cc_final: 0.1738 (ptp) REVERT: E 234 GLN cc_start: 0.2893 (OUTLIER) cc_final: 0.2584 (tt0) REVERT: E 240 GLN cc_start: 0.4458 (tt0) cc_final: 0.3659 (mm110) REVERT: E 320 MET cc_start: 0.7569 (mtm) cc_final: 0.7211 (mtm) REVERT: E 335 GLU cc_start: 0.3649 (mt-10) cc_final: 0.2981 (pt0) REVERT: E 357 ARG cc_start: 0.6725 (ptt-90) cc_final: 0.6429 (ptt180) REVERT: F 1 MET cc_start: 0.2647 (tpp) cc_final: 0.1333 (mmt) REVERT: F 67 GLN cc_start: 0.3640 (pp30) cc_final: 0.3032 (pp30) REVERT: F 77 MET cc_start: 0.5601 (mtt) cc_final: 0.5260 (mtt) REVERT: F 82 GLU cc_start: 0.2449 (OUTLIER) cc_final: 0.1845 (pm20) REVERT: F 112 ILE cc_start: 0.6372 (mm) cc_final: 0.5645 (tt) REVERT: F 201 MET cc_start: 0.1794 (tmm) cc_final: 0.0720 (ptp) REVERT: F 265 ASN cc_start: 0.6729 (t0) cc_final: 0.6253 (t0) REVERT: G 194 GLU cc_start: 0.3779 (OUTLIER) cc_final: 0.3300 (tt0) REVERT: H 1 MET cc_start: 0.3199 (ttp) cc_final: 0.1898 (ptp) REVERT: H 21 THR cc_start: 0.7114 (p) cc_final: 0.6847 (t) REVERT: H 75 ILE cc_start: 0.4627 (OUTLIER) cc_final: 0.4109 (mp) REVERT: H 137 LYS cc_start: 0.4432 (OUTLIER) cc_final: 0.3262 (ttmt) REVERT: H 201 MET cc_start: 0.3286 (tpp) cc_final: 0.2262 (mtp) REVERT: I 77 MET cc_start: 0.1652 (mmm) cc_final: 0.0232 (mtt) REVERT: I 79 HIS cc_start: 0.2013 (OUTLIER) cc_final: 0.1175 (m-70) REVERT: I 117 PHE cc_start: 0.3919 (m-10) cc_final: 0.3552 (m-80) REVERT: I 134 LEU cc_start: 0.2593 (OUTLIER) cc_final: 0.1976 (tt) REVERT: I 229 MET cc_start: 0.6325 (tmm) cc_final: 0.5995 (ttp) REVERT: I 232 PHE cc_start: 0.7225 (t80) cc_final: 0.6751 (t80) REVERT: I 236 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6945 (mp) REVERT: J 10 TYR cc_start: 0.4390 (OUTLIER) cc_final: 0.3834 (p90) REVERT: J 31 LYS cc_start: 0.3949 (mmtp) cc_final: 0.2911 (tttt) REVERT: J 229 MET cc_start: 0.5675 (tmm) cc_final: 0.5394 (tmm) REVERT: J 278 VAL cc_start: 0.5487 (m) cc_final: 0.5117 (m) REVERT: J 293 ARG cc_start: 0.5595 (tmt170) cc_final: 0.4810 (ptp-170) REVERT: K 1 MET cc_start: 0.3401 (OUTLIER) cc_final: 0.3170 (mtt) REVERT: K 229 MET cc_start: 0.7244 (tmm) cc_final: 0.6802 (ttp) REVERT: L 7 VAL cc_start: 0.6008 (t) cc_final: 0.5744 (p) REVERT: L 53 VAL cc_start: 0.3385 (OUTLIER) cc_final: 0.2993 (p) REVERT: L 231 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6364 (mt) REVERT: L 351 GLU cc_start: 0.4822 (mm-30) cc_final: 0.4503 (mm-30) REVERT: L 355 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6413 (mm-30) outliers start: 156 outliers final: 101 residues processed: 505 average time/residue: 0.2179 time to fit residues: 178.3702 Evaluate side-chains 457 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 341 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 321 GLU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 314 VAL Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 331 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 278 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 415 optimal weight: 20.0000 chunk 323 optimal weight: 9.9990 chunk 176 optimal weight: 0.0870 chunk 260 optimal weight: 20.0000 chunk 266 optimal weight: 5.9990 chunk 146 optimal weight: 0.2980 chunk 367 optimal weight: 20.0000 chunk 269 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 overall best weight: 2.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 151 ASN B 201 ASN B 407 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 GLN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 ASN K 346 HIS L 36 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.222245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.193622 restraints weight = 41823.535| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.43 r_work: 0.3879 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36160 Z= 0.144 Angle : 0.626 14.015 49145 Z= 0.304 Chirality : 0.050 0.217 5550 Planarity : 0.005 0.081 6322 Dihedral : 11.005 170.866 5063 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 3.84 % Allowed : 21.80 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 4469 helix: 0.61 (0.16), residues: 1071 sheet: -0.63 (0.16), residues: 1034 loop : -0.60 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 13 TYR 0.014 0.001 TYR F 10 PHE 0.038 0.002 PHE K 215 TRP 0.016 0.002 TRP B 282 HIS 0.008 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00337 (36140) covalent geometry : angle 0.62601 (49143) SS BOND : bond 0.00017 ( 1) SS BOND : angle 1.17883 ( 2) hydrogen bonds : bond 0.03563 ( 1052) hydrogen bonds : angle 5.22109 ( 3027) Misc. bond : bond 0.00286 ( 19) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 383 time to evaluate : 1.183 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 165 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7877 (mt) REVERT: A 349 ARG cc_start: 0.7726 (ptm160) cc_final: 0.7509 (ptt-90) REVERT: D 13 LYS cc_start: 0.7992 (mppt) cc_final: 0.7716 (mmmt) REVERT: D 192 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7589 (ttpp) REVERT: D 321 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 369 MET cc_start: 0.6479 (mmm) cc_final: 0.6188 (mmm) REVERT: C 368 ARG cc_start: 0.7337 (ttm170) cc_final: 0.7126 (ttm170) REVERT: C 390 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7613 (mmt180) REVERT: C 412 ARG cc_start: 0.7896 (ptt90) cc_final: 0.7518 (ptt180) REVERT: E 120 MET cc_start: 0.2539 (ttt) cc_final: 0.1768 (ptp) REVERT: E 171 ILE cc_start: 0.3659 (pt) cc_final: 0.3361 (mt) REVERT: E 240 GLN cc_start: 0.4425 (tt0) cc_final: 0.3730 (mm110) REVERT: E 320 MET cc_start: 0.7557 (mtm) cc_final: 0.7196 (mtm) REVERT: E 335 GLU cc_start: 0.3682 (mt-10) cc_final: 0.3004 (pt0) REVERT: E 357 ARG cc_start: 0.6517 (ptt-90) cc_final: 0.6257 (ptt180) REVERT: F 67 GLN cc_start: 0.3637 (pp30) cc_final: 0.3046 (pp30) REVERT: F 77 MET cc_start: 0.5612 (mtt) cc_final: 0.5388 (mtt) REVERT: F 201 MET cc_start: 0.1791 (tmm) cc_final: 0.0899 (ptp) REVERT: F 212 LEU cc_start: 0.2923 (mt) cc_final: 0.2192 (tp) REVERT: F 265 ASN cc_start: 0.6717 (t0) cc_final: 0.6123 (t0) REVERT: F 328 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7017 (pt0) REVERT: G 194 GLU cc_start: 0.3823 (OUTLIER) cc_final: 0.3311 (tt0) REVERT: G 198 PHE cc_start: 0.4435 (OUTLIER) cc_final: 0.2491 (t80) REVERT: H 1 MET cc_start: 0.3178 (ttp) cc_final: 0.2014 (ptp) REVERT: H 21 THR cc_start: 0.7146 (p) cc_final: 0.6929 (t) REVERT: H 69 GLN cc_start: 0.4592 (OUTLIER) cc_final: 0.4038 (mp10) REVERT: H 75 ILE cc_start: 0.4829 (OUTLIER) cc_final: 0.4302 (mp) REVERT: H 137 LYS cc_start: 0.4800 (OUTLIER) cc_final: 0.3378 (ttmt) REVERT: H 201 MET cc_start: 0.3406 (tpp) cc_final: 0.2276 (mtp) REVERT: H 329 ASP cc_start: 0.7324 (t0) cc_final: 0.6905 (m-30) REVERT: I 64 MET cc_start: 0.2732 (ptm) cc_final: 0.2462 (ptt) REVERT: I 77 MET cc_start: 0.1581 (mmm) cc_final: 0.0226 (mtt) REVERT: I 117 PHE cc_start: 0.3757 (m-10) cc_final: 0.3391 (m-80) REVERT: I 134 LEU cc_start: 0.2609 (OUTLIER) cc_final: 0.1976 (tt) REVERT: I 232 PHE cc_start: 0.7124 (t80) cc_final: 0.6711 (t80) REVERT: I 236 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6901 (mp) REVERT: J 2 LYS cc_start: 0.1464 (OUTLIER) cc_final: 0.0872 (ptpt) REVERT: J 10 TYR cc_start: 0.4298 (OUTLIER) cc_final: 0.3920 (p90) REVERT: J 31 LYS cc_start: 0.4155 (mmtp) cc_final: 0.3121 (tttt) REVERT: J 77 MET cc_start: 0.3540 (ptm) cc_final: 0.2642 (tmm) REVERT: J 229 MET cc_start: 0.5642 (tmm) cc_final: 0.5349 (tmm) REVERT: J 278 VAL cc_start: 0.5714 (m) cc_final: 0.5286 (m) REVERT: K 1 MET cc_start: 0.3440 (OUTLIER) cc_final: 0.3208 (mtt) REVERT: K 164 GLN cc_start: 0.3179 (tt0) cc_final: 0.2882 (tp40) REVERT: L 53 VAL cc_start: 0.3498 (OUTLIER) cc_final: 0.3112 (p) REVERT: L 206 GLN cc_start: 0.1829 (mm-40) cc_final: 0.1490 (mt0) REVERT: L 231 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6382 (mt) REVERT: L 351 GLU cc_start: 0.4733 (mm-30) cc_final: 0.4142 (mm-30) REVERT: L 355 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6517 (mm-30) outliers start: 156 outliers final: 110 residues processed: 513 average time/residue: 0.2255 time to fit residues: 185.3006 Evaluate side-chains 477 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 353 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 122 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 321 GLU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 314 VAL Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 331 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 99 optimal weight: 5.9990 chunk 240 optimal weight: 0.0060 chunk 221 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 424 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN D 51 GLN B 158 ASN C 51 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.222257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.193202 restraints weight = 41689.018| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.46 r_work: 0.3889 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36160 Z= 0.137 Angle : 0.615 13.754 49145 Z= 0.298 Chirality : 0.050 0.250 5550 Planarity : 0.006 0.311 6322 Dihedral : 10.872 171.028 5058 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 4.02 % Allowed : 22.08 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.12), residues: 4469 helix: 0.77 (0.16), residues: 1071 sheet: -0.67 (0.16), residues: 1027 loop : -0.59 (0.12), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG L 13 TYR 0.014 0.001 TYR F 10 PHE 0.019 0.002 PHE K 225 TRP 0.016 0.001 TRP B 282 HIS 0.007 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00323 (36140) covalent geometry : angle 0.61535 (49143) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.85604 ( 2) hydrogen bonds : bond 0.03441 ( 1052) hydrogen bonds : angle 5.17533 ( 3027) Misc. bond : bond 0.00265 ( 19) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 365 time to evaluate : 1.182 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 165 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7855 (mt) REVERT: A 294 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7076 (mmmt) REVERT: D 13 LYS cc_start: 0.7968 (mppt) cc_final: 0.7682 (mmmt) REVERT: D 175 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.7027 (pt) REVERT: D 192 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7429 (ttpp) REVERT: D 321 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7030 (mt-10) REVERT: C 174 PHE cc_start: 0.7828 (t80) cc_final: 0.7603 (t80) REVERT: C 368 ARG cc_start: 0.7359 (ttm170) cc_final: 0.7108 (ttm170) REVERT: C 390 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7655 (mmt180) REVERT: C 412 ARG cc_start: 0.7904 (ptt90) cc_final: 0.7523 (ptt180) REVERT: E 10 TYR cc_start: 0.5794 (OUTLIER) cc_final: 0.3660 (p90) REVERT: E 48 HIS cc_start: 0.1659 (OUTLIER) cc_final: 0.0983 (p90) REVERT: E 57 SER cc_start: 0.4242 (p) cc_final: 0.3655 (m) REVERT: E 120 MET cc_start: 0.2594 (ttt) cc_final: 0.1821 (ptp) REVERT: E 171 ILE cc_start: 0.3910 (pt) cc_final: 0.3347 (mt) REVERT: E 259 SER cc_start: 0.4040 (t) cc_final: 0.3571 (p) REVERT: E 320 MET cc_start: 0.7516 (mtm) cc_final: 0.7151 (mtm) REVERT: E 357 ARG cc_start: 0.6607 (ptt-90) cc_final: 0.6306 (ptt180) REVERT: F 1 MET cc_start: 0.2643 (tpp) cc_final: 0.0621 (ttt) REVERT: F 67 GLN cc_start: 0.3603 (pp30) cc_final: 0.3016 (pp30) REVERT: F 212 LEU cc_start: 0.2885 (mt) cc_final: 0.2180 (tp) REVERT: G 134 LEU cc_start: 0.3121 (OUTLIER) cc_final: 0.2913 (tt) REVERT: G 194 GLU cc_start: 0.3768 (OUTLIER) cc_final: 0.3331 (tt0) REVERT: G 198 PHE cc_start: 0.4396 (OUTLIER) cc_final: 0.2408 (t80) REVERT: H 1 MET cc_start: 0.3221 (ttp) cc_final: 0.2101 (ptp) REVERT: H 75 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4264 (mp) REVERT: H 201 MET cc_start: 0.3426 (tpp) cc_final: 0.2345 (mtp) REVERT: H 329 ASP cc_start: 0.7252 (t0) cc_final: 0.6846 (m-30) REVERT: I 77 MET cc_start: 0.1811 (mmm) cc_final: 0.0531 (mtt) REVERT: I 117 PHE cc_start: 0.3741 (m-10) cc_final: 0.3376 (m-80) REVERT: I 134 LEU cc_start: 0.2821 (OUTLIER) cc_final: 0.2170 (tt) REVERT: I 232 PHE cc_start: 0.7321 (t80) cc_final: 0.6920 (t80) REVERT: I 236 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6973 (mp) REVERT: J 10 TYR cc_start: 0.3989 (OUTLIER) cc_final: 0.3672 (p90) REVERT: J 77 MET cc_start: 0.3618 (ptm) cc_final: 0.2703 (tmm) REVERT: J 229 MET cc_start: 0.5643 (tmm) cc_final: 0.5325 (tmm) REVERT: J 278 VAL cc_start: 0.5577 (m) cc_final: 0.5279 (m) REVERT: K 1 MET cc_start: 0.3502 (OUTLIER) cc_final: 0.3292 (mtt) REVERT: K 164 GLN cc_start: 0.3375 (tt0) cc_final: 0.3142 (tp40) REVERT: L 53 VAL cc_start: 0.3316 (OUTLIER) cc_final: 0.2920 (p) REVERT: L 77 MET cc_start: 0.3455 (mtp) cc_final: 0.3233 (mtp) REVERT: L 207 LEU cc_start: 0.0929 (OUTLIER) cc_final: -0.0557 (mp) REVERT: L 231 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6282 (mt) REVERT: L 304 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: L 351 GLU cc_start: 0.4645 (mm-30) cc_final: 0.3430 (tp30) REVERT: L 355 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6478 (mm-30) outliers start: 163 outliers final: 121 residues processed: 500 average time/residue: 0.2179 time to fit residues: 175.6660 Evaluate side-chains 488 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 351 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 321 GLU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 314 VAL Chi-restraints excluded: chain J residue 320 MET Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 331 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 254 optimal weight: 10.0000 chunk 311 optimal weight: 0.0020 chunk 212 optimal weight: 1.9990 chunk 267 optimal weight: 8.9990 chunk 321 optimal weight: 7.9990 chunk 292 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN C 51 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS C 269 HIS E 48 HIS E 300 HIS ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 GLN ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 122 GLN L 300 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.221646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.191834 restraints weight = 41749.644| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.43 r_work: 0.3865 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36160 Z= 0.145 Angle : 0.622 13.683 49145 Z= 0.302 Chirality : 0.050 0.243 5550 Planarity : 0.006 0.239 6322 Dihedral : 11.061 171.176 5058 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.23 % Allowed : 21.95 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.12), residues: 4469 helix: 0.81 (0.16), residues: 1071 sheet: -0.94 (0.16), residues: 957 loop : -0.50 (0.12), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 272 TYR 0.016 0.001 TYR F 10 PHE 0.047 0.002 PHE K 215 TRP 0.016 0.002 TRP B 282 HIS 0.012 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00344 (36140) covalent geometry : angle 0.62224 (49143) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.82195 ( 2) hydrogen bonds : bond 0.03493 ( 1052) hydrogen bonds : angle 5.20658 ( 3027) Misc. bond : bond 0.00344 ( 19) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 362 time to evaluate : 1.233 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 165 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7828 (mt) REVERT: A 175 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7198 (pp) REVERT: A 294 LYS cc_start: 0.8113 (ptpt) cc_final: 0.7155 (mmmt) REVERT: D 175 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7114 (pt) REVERT: D 192 LYS cc_start: 0.7661 (ttpt) cc_final: 0.7395 (ttpp) REVERT: D 321 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7031 (mt-10) REVERT: C 174 PHE cc_start: 0.7816 (t80) cc_final: 0.7594 (t80) REVERT: C 368 ARG cc_start: 0.7378 (ttm170) cc_final: 0.7108 (ttm170) REVERT: C 390 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7662 (mmt180) REVERT: C 412 ARG cc_start: 0.7913 (ptt90) cc_final: 0.7528 (ptt180) REVERT: E 10 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.3833 (p90) REVERT: E 57 SER cc_start: 0.4346 (p) cc_final: 0.3585 (m) REVERT: E 120 MET cc_start: 0.2757 (ttt) cc_final: 0.1938 (ptp) REVERT: E 259 SER cc_start: 0.4101 (t) cc_final: 0.3627 (p) REVERT: E 293 ARG cc_start: 0.5172 (ptm160) cc_final: 0.4797 (ptp-170) REVERT: E 320 MET cc_start: 0.7592 (mtm) cc_final: 0.7213 (mtm) REVERT: F 1 MET cc_start: 0.2874 (tpp) cc_final: 0.0748 (ttt) REVERT: F 33 ILE cc_start: 0.6559 (mt) cc_final: 0.6307 (mt) REVERT: F 212 LEU cc_start: 0.2827 (mt) cc_final: 0.2239 (tp) REVERT: F 328 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7079 (pt0) REVERT: G 194 GLU cc_start: 0.3838 (OUTLIER) cc_final: 0.3276 (tt0) REVERT: G 198 PHE cc_start: 0.4273 (OUTLIER) cc_final: 0.2387 (t80) REVERT: H 1 MET cc_start: 0.3262 (ttp) cc_final: 0.2147 (ptp) REVERT: H 51 LEU cc_start: 0.3920 (OUTLIER) cc_final: 0.3605 (pp) REVERT: H 69 GLN cc_start: 0.4810 (OUTLIER) cc_final: 0.4508 (mt0) REVERT: H 75 ILE cc_start: 0.4747 (OUTLIER) cc_final: 0.4246 (mp) REVERT: H 92 LEU cc_start: 0.4170 (tp) cc_final: 0.3863 (tt) REVERT: H 201 MET cc_start: 0.3673 (OUTLIER) cc_final: 0.2311 (mtp) REVERT: H 329 ASP cc_start: 0.7374 (t0) cc_final: 0.6961 (m-30) REVERT: I 77 MET cc_start: 0.1137 (mmm) cc_final: 0.0512 (mtt) REVERT: I 90 LEU cc_start: 0.2847 (OUTLIER) cc_final: 0.2572 (tt) REVERT: I 117 PHE cc_start: 0.3708 (m-10) cc_final: 0.3324 (m-80) REVERT: I 134 LEU cc_start: 0.2850 (OUTLIER) cc_final: 0.2202 (tt) REVERT: I 232 PHE cc_start: 0.7353 (t80) cc_final: 0.6972 (t80) REVERT: I 236 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6948 (mp) REVERT: J 77 MET cc_start: 0.3624 (ptm) cc_final: 0.2679 (tmm) REVERT: J 229 MET cc_start: 0.5631 (tmm) cc_final: 0.5324 (tmm) REVERT: J 278 VAL cc_start: 0.5435 (m) cc_final: 0.5134 (m) REVERT: K 1 MET cc_start: 0.3374 (OUTLIER) cc_final: 0.3133 (mtt) REVERT: K 134 LEU cc_start: 0.4598 (tt) cc_final: 0.4262 (tp) REVERT: K 164 GLN cc_start: 0.3400 (tt0) cc_final: 0.3148 (tp40) REVERT: K 215 PHE cc_start: 0.5804 (t80) cc_final: 0.5215 (t80) REVERT: K 229 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6749 (ttp) REVERT: L 53 VAL cc_start: 0.3465 (OUTLIER) cc_final: 0.3187 (p) REVERT: L 207 LEU cc_start: 0.0916 (OUTLIER) cc_final: -0.0701 (mp) REVERT: L 304 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: L 351 GLU cc_start: 0.4610 (mm-30) cc_final: 0.3411 (tp30) REVERT: L 355 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6541 (mm-30) outliers start: 171 outliers final: 125 residues processed: 505 average time/residue: 0.2167 time to fit residues: 177.1380 Evaluate side-chains 496 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 352 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 321 GLU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 314 VAL Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 331 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 385 optimal weight: 30.0000 chunk 144 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 444 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN D 51 GLN C 51 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 HIS ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.221321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.192723 restraints weight = 41752.417| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.43 r_work: 0.3879 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36160 Z= 0.150 Angle : 0.633 13.656 49145 Z= 0.307 Chirality : 0.050 0.233 5550 Planarity : 0.006 0.144 6322 Dihedral : 11.058 171.464 5055 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.26 % Allowed : 22.21 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.12), residues: 4469 helix: 0.80 (0.16), residues: 1071 sheet: -1.25 (0.15), residues: 1127 loop : -0.50 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 13 TYR 0.021 0.001 TYR L 10 PHE 0.040 0.002 PHE K 215 TRP 0.017 0.002 TRP B 282 HIS 0.008 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00357 (36140) covalent geometry : angle 0.63277 (49143) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.73746 ( 2) hydrogen bonds : bond 0.03556 ( 1052) hydrogen bonds : angle 5.24164 ( 3027) Misc. bond : bond 0.00272 ( 19) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 357 time to evaluate : 1.333 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 1 MET cc_start: 0.7091 (tmm) cc_final: 0.6728 (tpp) REVERT: A 165 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 294 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7187 (mmmt) REVERT: D 175 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7134 (pt) REVERT: D 321 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7097 (mt-10) REVERT: C 174 PHE cc_start: 0.7818 (t80) cc_final: 0.7569 (t80) REVERT: C 368 ARG cc_start: 0.7356 (ttm170) cc_final: 0.7090 (ttm170) REVERT: C 390 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7676 (mmt180) REVERT: C 412 ARG cc_start: 0.7915 (ptt90) cc_final: 0.7538 (ptt180) REVERT: E 57 SER cc_start: 0.4478 (p) cc_final: 0.3702 (m) REVERT: E 81 GLU cc_start: 0.2904 (mp0) cc_final: 0.1871 (tt0) REVERT: E 120 MET cc_start: 0.3094 (ttt) cc_final: 0.1034 (ptp) REVERT: E 171 ILE cc_start: 0.3798 (pt) cc_final: 0.3583 (tt) REVERT: E 259 SER cc_start: 0.4311 (t) cc_final: 0.3773 (p) REVERT: E 293 ARG cc_start: 0.5337 (ptm160) cc_final: 0.4927 (ptp-170) REVERT: E 320 MET cc_start: 0.7569 (mtm) cc_final: 0.7166 (mtm) REVERT: F 1 MET cc_start: 0.2880 (tpp) cc_final: 0.0778 (ttp) REVERT: F 212 LEU cc_start: 0.2862 (mt) cc_final: 0.2326 (tp) REVERT: F 229 MET cc_start: 0.7375 (ttp) cc_final: 0.6820 (ttp) REVERT: F 328 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7120 (pt0) REVERT: G 33 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4889 (mt) REVERT: G 198 PHE cc_start: 0.4155 (OUTLIER) cc_final: 0.2302 (t80) REVERT: H 1 MET cc_start: 0.3628 (ttp) cc_final: 0.3194 (mtm) REVERT: H 51 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3615 (pp) REVERT: H 69 GLN cc_start: 0.4784 (OUTLIER) cc_final: 0.4452 (mt0) REVERT: H 75 ILE cc_start: 0.4636 (OUTLIER) cc_final: 0.4200 (mp) REVERT: H 92 LEU cc_start: 0.4191 (tp) cc_final: 0.3908 (tt) REVERT: H 201 MET cc_start: 0.3683 (OUTLIER) cc_final: 0.2449 (mtp) REVERT: H 329 ASP cc_start: 0.7419 (t0) cc_final: 0.7012 (m-30) REVERT: I 77 MET cc_start: 0.1363 (mmm) cc_final: 0.0904 (mtt) REVERT: I 90 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2616 (tt) REVERT: I 117 PHE cc_start: 0.3688 (m-10) cc_final: 0.3322 (m-80) REVERT: I 134 LEU cc_start: 0.2905 (OUTLIER) cc_final: 0.2266 (tt) REVERT: I 236 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6803 (mp) REVERT: J 2 LYS cc_start: 0.1703 (OUTLIER) cc_final: 0.1148 (ptpt) REVERT: J 77 MET cc_start: 0.3737 (ptm) cc_final: 0.2828 (tmm) REVERT: J 229 MET cc_start: 0.5694 (tmm) cc_final: 0.5400 (tmm) REVERT: J 278 VAL cc_start: 0.5391 (m) cc_final: 0.5122 (m) REVERT: K 1 MET cc_start: 0.3423 (OUTLIER) cc_final: 0.3189 (mtt) REVERT: K 134 LEU cc_start: 0.4585 (tt) cc_final: 0.4108 (tp) REVERT: K 164 GLN cc_start: 0.3399 (tt0) cc_final: 0.3155 (tp40) REVERT: K 189 GLN cc_start: 0.3416 (OUTLIER) cc_final: 0.2427 (mp10) REVERT: K 229 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6772 (ttp) REVERT: L 53 VAL cc_start: 0.3539 (OUTLIER) cc_final: 0.3250 (p) REVERT: L 231 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6187 (mt) REVERT: L 304 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: L 351 GLU cc_start: 0.4586 (mm-30) cc_final: 0.3381 (tp30) REVERT: L 355 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6582 (mm-30) outliers start: 172 outliers final: 129 residues processed: 499 average time/residue: 0.2210 time to fit residues: 178.4371 Evaluate side-chains 499 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 351 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 321 GLU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 342 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 266 CYS Chi-restraints excluded: chain J residue 320 MET Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 331 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 115 optimal weight: 8.9990 chunk 318 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 378 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 415 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN C 51 GLN C 130 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS C 199 GLN ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 GLN ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.217503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184758 restraints weight = 41463.611| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.47 r_work: 0.3777 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 36160 Z= 0.231 Angle : 0.738 14.553 49145 Z= 0.362 Chirality : 0.054 0.270 5550 Planarity : 0.007 0.200 6322 Dihedral : 11.499 173.079 5055 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.02 % Allowed : 22.70 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.12), residues: 4469 helix: 0.36 (0.16), residues: 1071 sheet: -0.78 (0.19), residues: 680 loop : -0.82 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 13 TYR 0.024 0.002 TYR F 10 PHE 0.034 0.003 PHE I 215 TRP 0.022 0.002 TRP B 282 HIS 0.010 0.002 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00560 (36140) covalent geometry : angle 0.73756 (49143) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.96439 ( 2) hydrogen bonds : bond 0.04185 ( 1052) hydrogen bonds : angle 5.63691 ( 3027) Misc. bond : bond 0.00332 ( 19) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 375 time to evaluate : 1.321 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 1 MET cc_start: 0.7168 (tmm) cc_final: 0.6777 (tpp) REVERT: A 165 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 175 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7285 (pp) REVERT: A 294 LYS cc_start: 0.8242 (ptpt) cc_final: 0.7146 (mmmt) REVERT: A 312 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7426 (m) REVERT: D 13 LYS cc_start: 0.7901 (mppt) cc_final: 0.7578 (mmmt) REVERT: D 175 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7294 (pt) REVERT: D 321 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7077 (mt-10) REVERT: B 78 LEU cc_start: 0.7439 (tp) cc_final: 0.7117 (mp) REVERT: C 412 ARG cc_start: 0.7937 (ptt90) cc_final: 0.7576 (ptt180) REVERT: E 81 GLU cc_start: 0.3343 (mp0) cc_final: 0.2312 (pt0) REVERT: E 210 MET cc_start: 0.1146 (ptm) cc_final: 0.0599 (ttt) REVERT: E 240 GLN cc_start: 0.4347 (tt0) cc_final: 0.3441 (mm110) REVERT: E 320 MET cc_start: 0.7571 (mtm) cc_final: 0.7200 (mtm) REVERT: F 1 MET cc_start: 0.3333 (tpp) cc_final: 0.1001 (ttm) REVERT: F 137 LYS cc_start: 0.3802 (mtpt) cc_final: 0.3372 (mmtm) REVERT: F 212 LEU cc_start: 0.2697 (mt) cc_final: 0.2196 (tp) REVERT: F 328 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: G 198 PHE cc_start: 0.4177 (OUTLIER) cc_final: 0.2504 (t80) REVERT: H 1 MET cc_start: 0.3648 (ttp) cc_final: 0.2694 (ptt) REVERT: H 51 LEU cc_start: 0.4045 (OUTLIER) cc_final: 0.3688 (pp) REVERT: H 69 GLN cc_start: 0.4895 (OUTLIER) cc_final: 0.4536 (mt0) REVERT: H 92 LEU cc_start: 0.4219 (tp) cc_final: 0.3867 (tt) REVERT: H 175 MET cc_start: 0.3388 (mmm) cc_final: 0.2979 (tpp) REVERT: H 201 MET cc_start: 0.3522 (OUTLIER) cc_final: 0.2167 (mtp) REVERT: I 77 MET cc_start: 0.2146 (mmm) cc_final: 0.0689 (mtt) REVERT: I 90 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2638 (tt) REVERT: I 117 PHE cc_start: 0.3812 (m-10) cc_final: 0.3446 (m-80) REVERT: I 134 LEU cc_start: 0.2986 (OUTLIER) cc_final: 0.2338 (tt) REVERT: I 236 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6788 (mp) REVERT: J 77 MET cc_start: 0.3759 (ptm) cc_final: 0.2861 (tmm) REVERT: J 229 MET cc_start: 0.5819 (tmm) cc_final: 0.5483 (tmm) REVERT: K 64 MET cc_start: 0.4810 (mmt) cc_final: 0.4410 (mmm) REVERT: K 164 GLN cc_start: 0.3555 (tt0) cc_final: 0.3130 (tp40) REVERT: K 189 GLN cc_start: 0.3311 (OUTLIER) cc_final: 0.2198 (mp10) REVERT: K 201 MET cc_start: 0.4216 (mpp) cc_final: 0.3770 (mpp) REVERT: K 215 PHE cc_start: 0.5934 (t80) cc_final: 0.5585 (t80) REVERT: K 229 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6702 (ttp) REVERT: L 53 VAL cc_start: 0.3784 (OUTLIER) cc_final: 0.3526 (p) REVERT: L 304 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: L 351 GLU cc_start: 0.4592 (mm-30) cc_final: 0.3992 (mm-30) REVERT: L 355 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6702 (mm-30) outliers start: 163 outliers final: 126 residues processed: 506 average time/residue: 0.2202 time to fit residues: 180.4248 Evaluate side-chains 500 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 358 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 321 GLU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 342 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 266 CYS Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 314 VAL Chi-restraints excluded: chain J residue 320 MET Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 56 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 331 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 362 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 200 optimal weight: 30.0000 chunk 390 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 423 optimal weight: 5.9990 chunk 368 optimal weight: 6.9990 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 74 GLN C 51 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.220821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.192157 restraints weight = 41697.007| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 1.40 r_work: 0.3881 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36160 Z= 0.146 Angle : 0.644 13.534 49145 Z= 0.312 Chirality : 0.050 0.221 5550 Planarity : 0.006 0.180 6322 Dihedral : 11.093 172.796 5055 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.55 % Allowed : 23.04 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.12), residues: 4469 helix: 0.60 (0.16), residues: 1071 sheet: -0.84 (0.19), residues: 690 loop : -0.71 (0.11), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 13 TYR 0.020 0.001 TYR F 10 PHE 0.036 0.002 PHE I 215 TRP 0.015 0.002 TRP B 282 HIS 0.008 0.001 HIS K 124 Details of bonding type rmsd covalent geometry : bond 0.00349 (36140) covalent geometry : angle 0.64412 (49143) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.66067 ( 2) hydrogen bonds : bond 0.03575 ( 1052) hydrogen bonds : angle 5.33812 ( 3027) Misc. bond : bond 0.00277 ( 19) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 372 time to evaluate : 1.230 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: K residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: L residue: PRO 199 >>> skipping REVERT: A 1 MET cc_start: 0.7085 (tmm) cc_final: 0.6729 (tpp) REVERT: A 165 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7785 (mt) REVERT: A 294 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7154 (mmmt) REVERT: A 312 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7379 (m) REVERT: D 13 LYS cc_start: 0.7937 (mppt) cc_final: 0.7647 (mmmt) REVERT: D 175 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7095 (pt) REVERT: D 321 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7052 (mt-10) REVERT: C 412 ARG cc_start: 0.7929 (ptt90) cc_final: 0.7594 (ptt180) REVERT: E 81 GLU cc_start: 0.3438 (mp0) cc_final: 0.2229 (pt0) REVERT: E 120 MET cc_start: 0.3036 (ttt) cc_final: 0.1917 (ptp) REVERT: E 171 ILE cc_start: 0.3700 (pt) cc_final: 0.3488 (tt) REVERT: E 210 MET cc_start: 0.1130 (ptm) cc_final: -0.0273 (tpp) REVERT: E 240 GLN cc_start: 0.4284 (tt0) cc_final: 0.3579 (mm110) REVERT: E 259 SER cc_start: 0.4545 (t) cc_final: 0.3888 (p) REVERT: E 293 ARG cc_start: 0.5293 (ptm160) cc_final: 0.4874 (ptp-170) REVERT: E 320 MET cc_start: 0.7512 (mtm) cc_final: 0.7128 (mtm) REVERT: F 1 MET cc_start: 0.3097 (tpp) cc_final: 0.1004 (ttp) REVERT: F 137 LYS cc_start: 0.3910 (mtpt) cc_final: 0.3518 (mmtm) REVERT: F 211 GLU cc_start: 0.3143 (mp0) cc_final: 0.2106 (mt-10) REVERT: F 212 LEU cc_start: 0.2380 (mt) cc_final: 0.1915 (tp) REVERT: F 229 MET cc_start: 0.7357 (ttp) cc_final: 0.7078 (ttp) REVERT: F 328 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: G 33 ILE cc_start: 0.5367 (OUTLIER) cc_final: 0.5053 (mt) REVERT: G 198 PHE cc_start: 0.4287 (OUTLIER) cc_final: 0.2536 (t80) REVERT: H 1 MET cc_start: 0.3546 (ttp) cc_final: 0.2654 (ptt) REVERT: H 51 LEU cc_start: 0.4096 (OUTLIER) cc_final: 0.3696 (pp) REVERT: H 69 GLN cc_start: 0.4816 (OUTLIER) cc_final: 0.4444 (mt0) REVERT: H 175 MET cc_start: 0.3019 (mmm) cc_final: 0.2736 (tpp) REVERT: H 201 MET cc_start: 0.3494 (OUTLIER) cc_final: 0.2314 (mtp) REVERT: I 77 MET cc_start: 0.2033 (mmm) cc_final: 0.0711 (mtt) REVERT: I 90 LEU cc_start: 0.2996 (OUTLIER) cc_final: 0.2707 (tt) REVERT: I 117 PHE cc_start: 0.3761 (m-10) cc_final: 0.3404 (m-80) REVERT: I 134 LEU cc_start: 0.2958 (OUTLIER) cc_final: 0.2316 (tt) REVERT: J 77 MET cc_start: 0.3864 (ptm) cc_final: 0.2926 (tmm) REVERT: J 229 MET cc_start: 0.5628 (tmm) cc_final: 0.5315 (tmm) REVERT: K 1 MET cc_start: 0.3425 (OUTLIER) cc_final: 0.2965 (mtt) REVERT: K 64 MET cc_start: 0.4602 (mmt) cc_final: 0.4213 (mmm) REVERT: K 164 GLN cc_start: 0.3472 (tt0) cc_final: 0.3189 (tp40) REVERT: K 189 GLN cc_start: 0.3469 (OUTLIER) cc_final: 0.2340 (mp10) REVERT: K 215 PHE cc_start: 0.6029 (t80) cc_final: 0.5698 (t80) REVERT: K 229 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6724 (ttp) REVERT: L 53 VAL cc_start: 0.3687 (OUTLIER) cc_final: 0.3405 (p) REVERT: L 304 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: L 351 GLU cc_start: 0.4351 (mm-30) cc_final: 0.3295 (tp30) REVERT: L 355 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6548 (mm-30) outliers start: 145 outliers final: 118 residues processed: 485 average time/residue: 0.2193 time to fit residues: 172.2613 Evaluate side-chains 495 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 361 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 235 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 SER Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 321 GLU Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 201 MET Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 342 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 266 CYS Chi-restraints excluded: chain J residue 314 VAL Chi-restraints excluded: chain J residue 320 MET Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 56 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 331 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 107 optimal weight: 3.9990 chunk 445 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 441 optimal weight: 20.0000 chunk 157 optimal weight: 0.7980 chunk 255 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 174 optimal weight: 0.1980 chunk 421 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN C 51 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.221187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.190932 restraints weight = 41357.164| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.53 r_work: 0.3867 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36160 Z= 0.118 Angle : 0.612 13.189 49145 Z= 0.295 Chirality : 0.049 0.215 5550 Planarity : 0.006 0.161 6322 Dihedral : 11.120 171.852 5055 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.17 % Allowed : 23.38 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.12), residues: 4469 helix: 0.85 (0.16), residues: 1072 sheet: -0.70 (0.19), residues: 682 loop : -0.60 (0.11), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 13 TYR 0.017 0.001 TYR F 10 PHE 0.025 0.002 PHE I 215 TRP 0.012 0.001 TRP B 282 HIS 0.008 0.001 HIS K 124 Details of bonding type rmsd covalent geometry : bond 0.00274 (36140) covalent geometry : angle 0.61194 (49143) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.57924 ( 2) hydrogen bonds : bond 0.03292 ( 1052) hydrogen bonds : angle 5.14865 ( 3027) Misc. bond : bond 0.00295 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9929.47 seconds wall clock time: 170 minutes 1.54 seconds (10201.54 seconds total)