Starting phenix.real_space_refine (version: dev) on Wed Dec 14 06:01:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/12_2022/6rbg_4798.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/12_2022/6rbg_4798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/12_2022/6rbg_4798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/12_2022/6rbg_4798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/12_2022/6rbg_4798.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbg_4798/12_2022/6rbg_4798.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 sd= 0.061 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 271": "OD1" <-> "OD2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E ASP 291": "OD1" <-> "OD2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F ASP 223": "OD1" <-> "OD2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F ASP 291": "OD1" <-> "OD2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G ASP 223": "OD1" <-> "OD2" Residue "G PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 271": "OD1" <-> "OD2" Residue "G ASP 291": "OD1" <-> "OD2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 271": "OD1" <-> "OD2" Residue "H ASP 291": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 19336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "B" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "C" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "D" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "E" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "F" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "G" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Chain: "H" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2417 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 297} Time building chain proxies: 10.41, per 1000 atoms: 0.54 Number of scatterers: 19336 At special positions: 0 Unit cell: (111.3, 111.3, 166.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3720 8.00 N 3344 7.00 C 12216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.10 Conformation dependent library (CDL) restraints added in 3.0 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 60.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA A 85 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.586A pdb=" N LYS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 183 through 210 removed outlier: 3.631A pdb=" N VAL A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 230 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 232' Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 155 " --> pdb=" O TYR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.706A pdb=" N LEU B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 230 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 231 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 232 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 232' Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 320 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA C 85 " --> pdb=" O GLY C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.588A pdb=" N LYS C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 183 through 210 removed outlier: 3.633A pdb=" N VAL C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE C 230 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 232' Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 80 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.632A pdb=" N GLN D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU D 229 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 230 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 231 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 232 " --> pdb=" O LEU D 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 226 through 232' Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.691A pdb=" N SER E 37 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 41 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 80 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA E 85 " --> pdb=" O GLY E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR E 94 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA E 102 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 160 removed outlier: 3.630A pdb=" N GLN E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL E 188 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG E 198 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU E 229 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE E 230 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 231 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 226 through 232' Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.602A pdb=" N LEU E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA E 302 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 313 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 320 " --> pdb=" O GLY E 316 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG E 321 " --> pdb=" O ARG E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER F 37 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 41 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 80 Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA F 85 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 removed outlier: 3.632A pdb=" N GLN F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 155 " --> pdb=" O TYR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS F 165 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN F 205 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.706A pdb=" N LEU F 229 " --> pdb=" O GLN F 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE F 230 " --> pdb=" O ASP F 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 232 " --> pdb=" O LEU F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 226 through 232' Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 238 through 243 Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 268 " --> pdb=" O ASP F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA F 302 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 313 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN F 318 " --> pdb=" O VAL F 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 320 " --> pdb=" O GLY F 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG F 321 " --> pdb=" O ARG F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 31 through 49 removed outlier: 3.692A pdb=" N SER G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 41 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.936A pdb=" N ALA G 85 " --> pdb=" O GLY G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.654A pdb=" N THR G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS G 165 " --> pdb=" O GLN G 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 180 Processing helix chain 'G' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL G 188 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 198 " --> pdb=" O ASP G 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN G 205 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 209 " --> pdb=" O GLN G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU G 229 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE G 230 " --> pdb=" O ASP G 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU G 231 " --> pdb=" O THR G 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 232 " --> pdb=" O LEU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 226 through 232' Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 238 through 243 Processing helix chain 'G' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU G 262 " --> pdb=" O THR G 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE G 265 " --> pdb=" O ASN G 261 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU G 268 " --> pdb=" O ASP G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 324 removed outlier: 3.861A pdb=" N ALA G 302 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 313 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN G 318 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU G 320 " --> pdb=" O GLY G 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 321 " --> pdb=" O ARG G 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 31 through 49 removed outlier: 3.691A pdb=" N SER H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA H 41 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 80 Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.937A pdb=" N ALA H 85 " --> pdb=" O GLY H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 96 removed outlier: 3.655A pdb=" N THR H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 104 removed outlier: 3.847A pdb=" N ALA H 102 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 removed outlier: 3.631A pdb=" N GLN H 153 " --> pdb=" O ALA H 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 155 " --> pdb=" O TYR H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 175 removed outlier: 3.587A pdb=" N LYS H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 180 Processing helix chain 'H' and resid 183 through 210 removed outlier: 3.632A pdb=" N VAL H 188 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 193 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG H 198 " --> pdb=" O ASP H 194 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN H 205 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 209 " --> pdb=" O GLN H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 232 removed outlier: 3.707A pdb=" N LEU H 229 " --> pdb=" O GLN H 226 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE H 230 " --> pdb=" O ASP H 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 231 " --> pdb=" O THR H 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 232 " --> pdb=" O LEU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 226 through 232' Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 238 through 243 Processing helix chain 'H' and resid 254 through 268 removed outlier: 3.603A pdb=" N LEU H 262 " --> pdb=" O THR H 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE H 265 " --> pdb=" O ASN H 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU H 268 " --> pdb=" O ASP H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 324 removed outlier: 3.860A pdb=" N ALA H 302 " --> pdb=" O THR H 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE H 313 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN H 318 " --> pdb=" O VAL H 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 320 " --> pdb=" O GLY H 316 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG H 321 " --> pdb=" O ARG H 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 3.623A pdb=" N TYR A 136 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 61 " --> pdb=" O VAL A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR B 136 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 61 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR C 136 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 61 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR D 136 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 61 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR E 136 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 61 " --> pdb=" O VAL E 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.624A pdb=" N TYR F 136 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 61 " --> pdb=" O VAL F 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.625A pdb=" N TYR G 136 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE G 61 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.623A pdb=" N TYR H 136 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE H 61 " --> pdb=" O VAL H 281 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6528 1.34 - 1.46: 3625 1.46 - 1.58: 9311 1.58 - 1.70: 0 1.70 - 1.81: 112 Bond restraints: 19576 Sorted by residual: bond pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS F 31 " pdb=" CA LYS F 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS H 31 " pdb=" CA LYS H 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N LYS A 31 " pdb=" CA LYS A 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" N LYS C 31 " pdb=" CA LYS C 31 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.20e-02 6.94e+03 1.05e+01 ... (remaining 19571 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.58: 537 107.58 - 114.75: 11843 114.75 - 121.92: 10165 121.92 - 129.09: 3911 129.09 - 136.26: 56 Bond angle restraints: 26512 Sorted by residual: angle pdb=" N LEU E 27 " pdb=" CA LEU E 27 " pdb=" C LEU E 27 " ideal model delta sigma weight residual 111.07 102.19 8.88 1.07e+00 8.73e-01 6.89e+01 angle pdb=" N LEU C 27 " pdb=" CA LEU C 27 " pdb=" C LEU C 27 " ideal model delta sigma weight residual 111.07 102.20 8.87 1.07e+00 8.73e-01 6.88e+01 angle pdb=" N LEU G 27 " pdb=" CA LEU G 27 " pdb=" C LEU G 27 " ideal model delta sigma weight residual 111.07 102.20 8.87 1.07e+00 8.73e-01 6.87e+01 angle pdb=" N LEU A 27 " pdb=" CA LEU A 27 " pdb=" C LEU A 27 " ideal model delta sigma weight residual 111.07 102.21 8.86 1.07e+00 8.73e-01 6.85e+01 angle pdb=" N LEU B 27 " pdb=" CA LEU B 27 " pdb=" C LEU B 27 " ideal model delta sigma weight residual 111.07 102.21 8.86 1.07e+00 8.73e-01 6.85e+01 ... (remaining 26507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 10799 16.80 - 33.61: 1097 33.61 - 50.41: 200 50.41 - 67.21: 24 67.21 - 84.01: 40 Dihedral angle restraints: 12160 sinusoidal: 4944 harmonic: 7216 Sorted by residual: dihedral pdb=" CA TYR D 280 " pdb=" C TYR D 280 " pdb=" N VAL D 281 " pdb=" CA VAL D 281 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR H 280 " pdb=" C TYR H 280 " pdb=" N VAL H 281 " pdb=" CA VAL H 281 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR F 280 " pdb=" C TYR F 280 " pdb=" N VAL F 281 " pdb=" CA VAL F 281 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 12157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2327 0.052 - 0.104: 690 0.104 - 0.156: 111 0.156 - 0.207: 0 0.207 - 0.259: 16 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CA GLN C 26 " pdb=" N GLN C 26 " pdb=" C GLN C 26 " pdb=" CB GLN C 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLN A 26 " pdb=" N GLN A 26 " pdb=" C GLN A 26 " pdb=" CB GLN A 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLN G 26 " pdb=" N GLN G 26 " pdb=" C GLN G 26 " pdb=" CB GLN G 26 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3141 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C LEU H 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU H 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL H 25 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C LEU A 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU A 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 25 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 24 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C LEU C 24 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU C 24 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 25 " 0.016 2.00e-02 2.50e+03 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 7024 2.91 - 3.40: 18140 3.40 - 3.90: 28989 3.90 - 4.40: 34530 4.40 - 4.90: 56348 Nonbonded interactions: 145031 Sorted by model distance: nonbonded pdb=" O LEU F 23 " pdb=" OE1 GLN F 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU G 23 " pdb=" OE1 GLN G 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU C 23 " pdb=" OE1 GLN C 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU E 23 " pdb=" OE1 GLN E 26 " model vdw 2.407 3.040 nonbonded pdb=" O LEU A 23 " pdb=" OE1 GLN A 26 " model vdw 2.407 3.040 ... (remaining 145026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 12216 2.51 5 N 3344 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.060 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.150 Process input model: 47.010 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.004 0.050 19576 Z= 0.281 Angle : 0.890 9.658 26512 Z= 0.513 Chirality : 0.050 0.259 3144 Planarity : 0.005 0.038 3432 Dihedral : 14.499 84.014 7488 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.39 (0.11), residues: 2448 helix: -5.01 (0.04), residues: 1496 sheet: -3.47 (0.31), residues: 200 loop : -1.98 (0.19), residues: 752 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 339 time to evaluate : 2.286 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 347 average time/residue: 1.1995 time to fit residues: 470.7821 Evaluate side-chains 177 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 0.0040 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 318 ASN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 318 ASN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 ASN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 GLN E 318 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN G 318 ASN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 19576 Z= 0.333 Angle : 0.618 8.042 26512 Z= 0.317 Chirality : 0.039 0.117 3144 Planarity : 0.004 0.023 3432 Dihedral : 5.226 18.386 2656 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.13), residues: 2448 helix: -3.38 (0.08), residues: 1568 sheet: -2.56 (0.36), residues: 200 loop : -1.54 (0.21), residues: 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 142 time to evaluate : 2.414 Fit side-chains outliers start: 84 outliers final: 29 residues processed: 206 average time/residue: 1.0481 time to fit residues: 250.4662 Evaluate side-chains 156 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 3.1627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.4980 chunk 235 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 19576 Z= 0.216 Angle : 0.515 7.578 26512 Z= 0.261 Chirality : 0.037 0.113 3144 Planarity : 0.002 0.018 3432 Dihedral : 4.738 17.241 2656 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.16), residues: 2448 helix: -2.15 (0.11), residues: 1600 sheet: -1.65 (0.38), residues: 208 loop : -0.90 (0.23), residues: 640 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 170 time to evaluate : 2.403 Fit side-chains outliers start: 62 outliers final: 35 residues processed: 214 average time/residue: 1.2144 time to fit residues: 295.7769 Evaluate side-chains 167 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 2.290 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 29 residues processed: 7 average time/residue: 0.4775 time to fit residues: 7.6818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 219 optimal weight: 0.0970 chunk 231 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 19576 Z= 0.171 Angle : 0.487 7.347 26512 Z= 0.245 Chirality : 0.036 0.110 3144 Planarity : 0.002 0.013 3432 Dihedral : 4.456 16.705 2656 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2448 helix: -1.37 (0.13), residues: 1600 sheet: -1.20 (0.39), residues: 208 loop : -0.58 (0.23), residues: 640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 151 time to evaluate : 2.531 Fit side-chains outliers start: 66 outliers final: 28 residues processed: 199 average time/residue: 1.1354 time to fit residues: 260.2344 Evaluate side-chains 161 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.9222 time to fit residues: 6.3670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 172 optimal weight: 0.0000 chunk 95 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 19576 Z= 0.176 Angle : 0.477 7.910 26512 Z= 0.240 Chirality : 0.036 0.111 3144 Planarity : 0.002 0.014 3432 Dihedral : 4.306 16.511 2656 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2448 helix: -0.86 (0.13), residues: 1600 sheet: -1.00 (0.39), residues: 208 loop : -0.46 (0.23), residues: 640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 155 time to evaluate : 2.408 Fit side-chains outliers start: 80 outliers final: 28 residues processed: 214 average time/residue: 1.0590 time to fit residues: 262.5754 Evaluate side-chains 154 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.1741 time to fit residues: 4.3179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 232 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 19576 Z= 0.186 Angle : 0.485 8.979 26512 Z= 0.242 Chirality : 0.037 0.111 3144 Planarity : 0.002 0.015 3432 Dihedral : 4.253 16.559 2656 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2448 helix: -0.50 (0.14), residues: 1600 sheet: -0.80 (0.40), residues: 208 loop : -0.37 (0.23), residues: 640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 2.264 Fit side-chains outliers start: 43 outliers final: 27 residues processed: 171 average time/residue: 0.9995 time to fit residues: 200.0053 Evaluate side-chains 154 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 7 average time/residue: 0.5941 time to fit residues: 8.3633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 132 optimal weight: 0.0040 chunk 169 optimal weight: 0.4980 chunk 131 optimal weight: 0.0570 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 231 optimal weight: 0.5980 chunk 144 optimal weight: 0.4980 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.2310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 260 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN G 260 GLN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 19576 Z= 0.114 Angle : 0.460 10.124 26512 Z= 0.229 Chirality : 0.035 0.109 3144 Planarity : 0.002 0.014 3432 Dihedral : 4.021 15.877 2656 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2448 helix: 0.13 (0.14), residues: 1568 sheet: -0.68 (0.40), residues: 208 loop : -0.28 (0.22), residues: 672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 2.157 Fit side-chains outliers start: 33 outliers final: 16 residues processed: 185 average time/residue: 1.0168 time to fit residues: 219.2879 Evaluate side-chains 148 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 3.2202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 19576 Z= 0.240 Angle : 0.526 10.816 26512 Z= 0.257 Chirality : 0.038 0.113 3144 Planarity : 0.002 0.018 3432 Dihedral : 4.164 16.628 2656 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2448 helix: 0.06 (0.14), residues: 1600 sheet: -0.36 (0.40), residues: 200 loop : -0.30 (0.22), residues: 648 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 2.489 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 160 average time/residue: 1.0028 time to fit residues: 188.3640 Evaluate side-chains 144 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 1.1732 time to fit residues: 5.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 10.0000 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 129 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 194 optimal weight: 0.0980 chunk 203 optimal weight: 0.0870 chunk 214 optimal weight: 0.9980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 19576 Z= 0.131 Angle : 0.482 11.450 26512 Z= 0.238 Chirality : 0.035 0.113 3144 Planarity : 0.002 0.014 3432 Dihedral : 3.984 15.906 2656 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2448 helix: 0.54 (0.14), residues: 1576 sheet: -0.27 (0.40), residues: 200 loop : -0.38 (0.21), residues: 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 2.322 Fit side-chains outliers start: 29 outliers final: 23 residues processed: 170 average time/residue: 0.9331 time to fit residues: 187.6394 Evaluate side-chains 157 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 2.184 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 3.1929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 190 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 19576 Z= 0.204 Angle : 0.517 11.654 26512 Z= 0.252 Chirality : 0.037 0.111 3144 Planarity : 0.002 0.016 3432 Dihedral : 4.060 16.157 2656 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2448 helix: 0.47 (0.14), residues: 1600 sheet: -0.22 (0.40), residues: 200 loop : -0.31 (0.22), residues: 648 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 2.301 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 164 average time/residue: 0.9337 time to fit residues: 181.3477 Evaluate side-chains 151 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 2.296 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 3.1528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.1980 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 190 optimal weight: 0.0370 chunk 79 optimal weight: 0.3980 chunk 195 optimal weight: 0.0010 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 218 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098653 restraints weight = 25216.119| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.33 r_work: 0.3081 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 19576 Z= 0.122 Angle : 0.485 12.452 26512 Z= 0.238 Chirality : 0.035 0.111 3144 Planarity : 0.002 0.016 3432 Dihedral : 3.881 15.779 2656 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2448 helix: 0.97 (0.15), residues: 1576 sheet: -0.14 (0.39), residues: 200 loop : -0.35 (0.21), residues: 672 =============================================================================== Job complete usr+sys time: 5101.84 seconds wall clock time: 92 minutes 12.21 seconds (5532.21 seconds total)