Starting phenix.real_space_refine on Fri Aug 9 10:19:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/08_2024/6o9z_0664_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/08_2024/6o9z_0664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/08_2024/6o9z_0664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/08_2024/6o9z_0664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/08_2024/6o9z_0664_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/08_2024/6o9z_0664_neut.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.011 sd= 0.787 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 2 5.49 5 S 124 5.16 5 C 16584 2.51 5 N 4335 2.21 5 O 4743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C ASP 301": "OD1" <-> "OD2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ASP 459": "OD1" <-> "OD2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F ASP 459": "OD1" <-> "OD2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G ASP 248": "OD1" <-> "OD2" Residue "G GLU 299": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "H ASP 158": "OD1" <-> "OD2" Residue "H ASP 248": "OD1" <-> "OD2" Residue "H GLU 299": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "M ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25788 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3172 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 407} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3172 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 407} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 151 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2415 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 20, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2425 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 20, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2683 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 65 Chain: "F" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2683 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 65 Chain: "G" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2080 Classifications: {'peptide': 290} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "H" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2080 Classifications: {'peptide': 290} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 185 Chain: "J" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 185 Chain: "L" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 930 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 148} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 313 Chain: "M" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 930 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 148} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 313 Time building chain proxies: 15.50, per 1000 atoms: 0.60 Number of scatterers: 25788 At special positions: 0 Unit cell: (186.594, 171.798, 120.012, 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 124 16.00 P 2 15.00 O 4743 8.00 N 4335 7.00 C 16584 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: 10.49 Conformation dependent library (CDL) restraints added in 5.5 seconds 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6850 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 34 sheets defined 43.8% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 98 through 108 removed outlier: 4.189A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.704A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 98 through 108 removed outlier: 4.190A pdb=" N LYS B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.704A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.616A pdb=" N MET C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.796A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.779A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 208 removed outlier: 3.572A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 296 through 304 removed outlier: 4.440A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.771A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.670A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 126 through 145 removed outlier: 3.574A pdb=" N GLN D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 155 through 158 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 208 removed outlier: 3.738A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.513A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.869A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 239 Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.809A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 312 through 325 removed outlier: 3.673A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'E' and resid 368 through 379 removed outlier: 3.889A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 418 through 430 removed outlier: 4.462A pdb=" N GLN E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.727A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 518 removed outlier: 3.718A pdb=" N VAL E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.869A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 239 Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.809A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 325 removed outlier: 3.673A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 353 Processing helix chain 'F' and resid 368 through 379 removed outlier: 3.888A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 418 through 430 removed outlier: 4.462A pdb=" N GLN F 422 " --> pdb=" O VAL F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 463 removed outlier: 3.726A pdb=" N LEU F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 518 removed outlier: 3.717A pdb=" N VAL F 518 " --> pdb=" O VAL F 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 16 Processing helix chain 'G' and resid 21 through 36 removed outlier: 3.705A pdb=" N ALA G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 60 removed outlier: 3.517A pdb=" N ASP G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 77 removed outlier: 4.106A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 116 removed outlier: 4.011A pdb=" N ARG G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.831A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 222 Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 292 through 305 Processing helix chain 'H' and resid 3 through 16 Processing helix chain 'H' and resid 21 through 36 removed outlier: 3.705A pdb=" N ALA H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 60 removed outlier: 3.518A pdb=" N ASP H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 77 removed outlier: 4.106A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 116 removed outlier: 4.011A pdb=" N ARG H 108 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 179 through 183 removed outlier: 3.831A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 222 Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 292 through 305 Processing helix chain 'I' and resid 36 through 46 removed outlier: 3.574A pdb=" N VAL I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 68 removed outlier: 4.015A pdb=" N GLU I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 removed outlier: 3.917A pdb=" N ILE I 93 " --> pdb=" O SER I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 97 removed outlier: 3.670A pdb=" N LEU I 97 " --> pdb=" O TYR I 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 94 through 97' Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.655A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.635A pdb=" N LEU I 187 " --> pdb=" O LYS I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.674A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 236 Processing helix chain 'I' and resid 282 through 292 removed outlier: 3.909A pdb=" N ARG I 286 " --> pdb=" O TRP I 282 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 46 removed outlier: 3.574A pdb=" N VAL J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 68 removed outlier: 4.016A pdb=" N GLU J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 removed outlier: 3.917A pdb=" N ILE J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 97 removed outlier: 3.669A pdb=" N LEU J 97 " --> pdb=" O TYR J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 94 through 97' Processing helix chain 'J' and resid 114 through 124 removed outlier: 3.654A pdb=" N VAL J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.634A pdb=" N LEU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.675A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 236 Processing helix chain 'J' and resid 282 through 292 removed outlier: 3.910A pdb=" N ARG J 286 " --> pdb=" O TRP J 282 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP J 290 " --> pdb=" O ARG J 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 52 Processing helix chain 'L' and resid 90 through 118 Processing helix chain 'L' and resid 122 through 142 removed outlier: 3.510A pdb=" N LEU L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 158 removed outlier: 3.650A pdb=" N TYR L 149 " --> pdb=" O GLY L 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 157 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 163 Processing helix chain 'L' and resid 168 through 180 removed outlier: 3.614A pdb=" N ARG L 172 " --> pdb=" O ASN L 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 52 Processing helix chain 'M' and resid 90 through 118 Processing helix chain 'M' and resid 122 through 142 removed outlier: 3.510A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 158 removed outlier: 3.651A pdb=" N TYR M 149 " --> pdb=" O GLY M 145 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER M 157 " --> pdb=" O LYS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 168 through 180 removed outlier: 3.615A pdb=" N ARG M 172 " --> pdb=" O ASN M 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 removed outlier: 7.515A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA A 45 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE A 94 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 47 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN A 44 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL A 151 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 46 " --> pdb=" O VAL A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 246 removed outlier: 4.684A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA A 204 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE A 215 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 202 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY I 159 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.621A pdb=" N PHE A 224 " --> pdb=" O ILE I 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 removed outlier: 6.683A pdb=" N TYR A 343 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.382A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.864A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.057A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 458 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 450 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.515A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA B 45 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE B 94 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 47 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN B 44 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL B 151 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 46 " --> pdb=" O VAL B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'B' and resid 244 through 246 removed outlier: 4.683A pdb=" N ILE B 287 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 204 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE B 215 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 202 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.596A pdb=" N PHE B 224 " --> pdb=" O ILE J 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.683A pdb=" N TYR B 343 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.381A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.864A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS B 384 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 411 through 413 removed outlier: 6.057A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 458 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 450 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.610A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 189 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET C 217 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 191 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AC1, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.166A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL F 358 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU F 386 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL F 360 " --> pdb=" O LEU F 386 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.052A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL D 189 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET D 217 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL D 191 " --> pdb=" O MET D 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AC4, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.160A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL E 358 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU E 386 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL E 360 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC6, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC7, first strand: chain 'G' and resid 175 through 178 removed outlier: 8.545A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA G 123 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR G 151 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE G 125 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR G 153 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR G 127 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AC9, first strand: chain 'H' and resid 175 through 178 removed outlier: 8.546A pdb=" N THR H 176 " --> pdb=" O PHE H 148 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA H 123 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR H 151 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE H 125 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR H 153 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR H 127 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD2, first strand: chain 'I' and resid 75 through 78 removed outlier: 8.531A pdb=" N ILE I 52 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL I 54 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL I 7 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 200 through 201 removed outlier: 6.429A pdb=" N LEU I 128 " --> pdb=" O TYR I 264 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE I 266 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET I 130 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 75 through 78 removed outlier: 8.530A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 200 through 201 removed outlier: 6.430A pdb=" N LEU J 128 " --> pdb=" O TYR J 264 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE J 266 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET J 130 " --> pdb=" O PHE J 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 18 through 26 removed outlier: 6.912A pdb=" N TYR L 32 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE L 26 " --> pdb=" O GLY L 30 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU L 42 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU L 84 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET L 44 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER L 85 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL L 72 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 18 through 26 removed outlier: 6.913A pdb=" N TYR M 32 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE M 26 " --> pdb=" O GLY M 30 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY M 30 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLU M 42 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU M 84 " --> pdb=" O GLU M 42 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET M 44 " --> pdb=" O LEU M 84 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER M 85 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL M 72 " --> pdb=" O SER M 85 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3315 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: 9.14 Time building geometry restraints manager: 11.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8528 1.34 - 1.46: 4992 1.46 - 1.58: 12495 1.58 - 1.70: 8 1.70 - 1.81: 190 Bond restraints: 26213 Sorted by residual: bond pdb=" CD2 TRP A 97 " pdb=" CE2 TRP A 97 " ideal model delta sigma weight residual 1.409 1.445 -0.036 1.70e-02 3.46e+03 4.37e+00 bond pdb=" CD2 TRP C 51 " pdb=" CE2 TRP C 51 " ideal model delta sigma weight residual 1.409 1.444 -0.035 1.70e-02 3.46e+03 4.32e+00 bond pdb=" CD2 TRP B 97 " pdb=" CE2 TRP B 97 " ideal model delta sigma weight residual 1.409 1.444 -0.035 1.70e-02 3.46e+03 4.21e+00 bond pdb=" CD2 TRP D 51 " pdb=" CE2 TRP D 51 " ideal model delta sigma weight residual 1.409 1.443 -0.034 1.70e-02 3.46e+03 4.01e+00 bond pdb=" CD2 TRP F 476 " pdb=" CE2 TRP F 476 " ideal model delta sigma weight residual 1.409 1.441 -0.032 1.70e-02 3.46e+03 3.52e+00 ... (remaining 26208 not shown) Histogram of bond angle deviations from ideal: 97.68 - 104.90: 472 104.90 - 112.11: 13799 112.11 - 119.33: 8538 119.33 - 126.54: 12519 126.54 - 133.76: 271 Bond angle restraints: 35599 Sorted by residual: angle pdb=" N GLN G 156 " pdb=" CA GLN G 156 " pdb=" C GLN G 156 " ideal model delta sigma weight residual 109.81 119.94 -10.13 2.21e+00 2.05e-01 2.10e+01 angle pdb=" N GLN H 156 " pdb=" CA GLN H 156 " pdb=" C GLN H 156 " ideal model delta sigma weight residual 109.81 119.94 -10.13 2.21e+00 2.05e-01 2.10e+01 angle pdb=" N ALA G 295 " pdb=" CA ALA G 295 " pdb=" C ALA G 295 " ideal model delta sigma weight residual 113.23 107.63 5.60 1.24e+00 6.50e-01 2.04e+01 angle pdb=" N ALA H 295 " pdb=" CA ALA H 295 " pdb=" C ALA H 295 " ideal model delta sigma weight residual 113.23 107.65 5.58 1.24e+00 6.50e-01 2.03e+01 angle pdb=" N CYS H 57 " pdb=" CA CYS H 57 " pdb=" C CYS H 57 " ideal model delta sigma weight residual 113.41 108.22 5.19 1.22e+00 6.72e-01 1.81e+01 ... (remaining 35594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 14776 17.32 - 34.65: 831 34.65 - 51.97: 147 51.97 - 69.30: 38 69.30 - 86.62: 27 Dihedral angle restraints: 15819 sinusoidal: 5384 harmonic: 10435 Sorted by residual: dihedral pdb=" CA ASN D 242 " pdb=" C ASN D 242 " pdb=" N GLY D 243 " pdb=" CA GLY D 243 " ideal model delta harmonic sigma weight residual 180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LYS G 209 " pdb=" C LYS G 209 " pdb=" N ILE G 210 " pdb=" CA ILE G 210 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LYS H 209 " pdb=" C LYS H 209 " pdb=" N ILE H 210 " pdb=" CA ILE H 210 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 15816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3329 0.060 - 0.119: 938 0.119 - 0.179: 103 0.179 - 0.238: 15 0.238 - 0.298: 2 Chirality restraints: 4387 Sorted by residual: chirality pdb=" CB VAL G 236 " pdb=" CA VAL G 236 " pdb=" CG1 VAL G 236 " pdb=" CG2 VAL G 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB VAL H 236 " pdb=" CA VAL H 236 " pdb=" CG1 VAL H 236 " pdb=" CG2 VAL H 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA MET H 1 " pdb=" N MET H 1 " pdb=" C MET H 1 " pdb=" CB MET H 1 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4384 not shown) Planarity restraints: 4526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 294 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.69e+01 pdb=" C SER H 294 " 0.071 2.00e-02 2.50e+03 pdb=" O SER H 294 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA H 295 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 294 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C SER G 294 " 0.071 2.00e-02 2.50e+03 pdb=" O SER G 294 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA G 295 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 368 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU E 368 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU E 368 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY E 369 " 0.019 2.00e-02 2.50e+03 ... (remaining 4523 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3076 2.73 - 3.28: 25377 3.28 - 3.82: 42446 3.82 - 4.36: 49353 4.36 - 4.90: 86023 Nonbonded interactions: 206275 Sorted by model distance: nonbonded pdb=" OE1 GLU D 193 " pdb=" NE2 HIS D 201 " model vdw 2.192 3.120 nonbonded pdb=" OG1 THR F 440 " pdb=" OE2 GLU F 503 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR E 440 " pdb=" OE2 GLU E 503 " model vdw 2.236 3.040 nonbonded pdb=" NE2 GLN H 243 " pdb=" O TYR H 275 " model vdw 2.238 3.120 nonbonded pdb=" NE2 GLN G 243 " pdb=" O TYR G 275 " model vdw 2.239 3.120 ... (remaining 206270 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' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 73.310 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.008 0.071 26213 Z= 0.522 Angle : 0.929 11.048 35599 Z= 0.522 Chirality : 0.054 0.298 4387 Planarity : 0.007 0.057 4526 Dihedral : 12.406 86.619 8969 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.48 % Allowed : 5.13 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.03 (0.12), residues: 3555 helix: -1.78 (0.11), residues: 1387 sheet: -2.11 (0.22), residues: 471 loop : -2.10 (0.13), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 37 HIS 0.011 0.002 HIS B 105 PHE 0.036 0.003 PHE H 239 TYR 0.022 0.002 TYR D 335 ARG 0.003 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 763 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7510 (t0) cc_final: 0.7110 (t0) REVERT: A 276 LEU cc_start: 0.8888 (tp) cc_final: 0.8677 (tp) REVERT: A 312 ASP cc_start: 0.7983 (m-30) cc_final: 0.7702 (m-30) REVERT: B 50 ASP cc_start: 0.7656 (t0) cc_final: 0.7269 (t0) REVERT: C 20 GLU cc_start: 0.8684 (tt0) cc_final: 0.7676 (tm-30) REVERT: C 44 GLN cc_start: 0.8018 (tt0) cc_final: 0.7745 (tt0) REVERT: C 48 ASP cc_start: 0.8029 (m-30) cc_final: 0.7755 (m-30) REVERT: C 68 MET cc_start: 0.8423 (mtp) cc_final: 0.7707 (ttp) REVERT: C 96 LEU cc_start: 0.7568 (mt) cc_final: 0.7359 (tt) REVERT: C 163 GLU cc_start: 0.7479 (tt0) cc_final: 0.7176 (tt0) REVERT: C 209 LYS cc_start: 0.9138 (mttt) cc_final: 0.8911 (mtmt) REVERT: C 237 LYS cc_start: 0.8490 (tptt) cc_final: 0.8242 (tptp) REVERT: D 44 GLN cc_start: 0.8007 (tt0) cc_final: 0.7766 (tt0) REVERT: D 242 ASN cc_start: 0.8588 (m110) cc_final: 0.8235 (m-40) REVERT: E 236 VAL cc_start: 0.9101 (t) cc_final: 0.8847 (t) REVERT: E 362 ASP cc_start: 0.8445 (t0) cc_final: 0.8239 (t0) REVERT: E 439 GLU cc_start: 0.8692 (mp0) cc_final: 0.8115 (mp0) REVERT: E 462 ASP cc_start: 0.8437 (m-30) cc_final: 0.8205 (m-30) REVERT: F 236 VAL cc_start: 0.9100 (t) cc_final: 0.8850 (t) REVERT: F 362 ASP cc_start: 0.8436 (t0) cc_final: 0.8184 (t70) REVERT: F 367 LEU cc_start: 0.9186 (mt) cc_final: 0.8975 (mm) REVERT: F 439 GLU cc_start: 0.8701 (mp0) cc_final: 0.8125 (mp0) REVERT: F 462 ASP cc_start: 0.8433 (m-30) cc_final: 0.8190 (m-30) REVERT: G 17 ASP cc_start: 0.8305 (t0) cc_final: 0.8046 (t0) REVERT: G 75 PHE cc_start: 0.8835 (t80) cc_final: 0.8291 (t80) REVERT: G 187 MET cc_start: 0.8889 (tpp) cc_final: 0.8604 (tpt) REVERT: G 244 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8287 (tp40) REVERT: G 245 ASP cc_start: 0.8804 (t0) cc_final: 0.8455 (t0) REVERT: G 290 VAL cc_start: 0.9384 (t) cc_final: 0.9074 (t) REVERT: H 17 ASP cc_start: 0.8312 (t0) cc_final: 0.8079 (t0) REVERT: H 75 PHE cc_start: 0.8861 (t80) cc_final: 0.8281 (t80) REVERT: H 187 MET cc_start: 0.8886 (tpp) cc_final: 0.8471 (tpt) REVERT: H 244 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8274 (tp40) REVERT: H 245 ASP cc_start: 0.8854 (t0) cc_final: 0.8521 (t0) REVERT: H 290 VAL cc_start: 0.9357 (t) cc_final: 0.8953 (t) REVERT: I 125 ASP cc_start: 0.8826 (t70) cc_final: 0.8527 (t0) REVERT: I 161 ASP cc_start: 0.7032 (t70) cc_final: 0.6816 (p0) REVERT: J 125 ASP cc_start: 0.8774 (t70) cc_final: 0.8484 (t0) outliers start: 12 outliers final: 2 residues processed: 769 average time/residue: 0.3240 time to fit residues: 402.6113 Evaluate side-chains 554 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 552 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 323 optimal weight: 50.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: