Starting phenix.real_space_refine on Tue Dec 12 18:32:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/12_2023/6ebk_9024_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/12_2023/6ebk_9024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/12_2023/6ebk_9024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/12_2023/6ebk_9024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/12_2023/6ebk_9024_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/12_2023/6ebk_9024_neut_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.003 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 12 5.49 5 S 120 5.16 5 C 14240 2.51 5 N 3728 2.21 5 O 4112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 284": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "H PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 22212 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2925 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 159 Chain: "C" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2925 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "F" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2925 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 159 Chain: "G" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "H" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2925 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 12.69, per 1000 atoms: 0.57 Number of scatterers: 22212 At special positions: 0 Unit cell: (131.095, 131.095, 161.99, 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 120 16.00 P 12 15.00 O 4112 8.00 N 3728 7.00 C 14240 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: 9.45 Conformation dependent library (CDL) restraints added in 4.1 seconds 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 16 sheets defined 53.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.523A pdb=" N ASN A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 106 removed outlier: 6.234A pdb=" N ALA A 95 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 98 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 104 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 106 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.680A pdb=" N GLU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.501A pdb=" N ALA A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.775A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 257 removed outlier: 4.502A pdb=" N SER A 257 " --> pdb=" O LYS A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 257' Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.520A pdb=" N GLN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 327 through 336 removed outlier: 3.901A pdb=" N ALA A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.893A pdb=" N GLN B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 68 Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.845A pdb=" N TYR B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.644A pdb=" N GLU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.576A pdb=" N MET B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.576A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 184 removed outlier: 3.814A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.660A pdb=" N CYS B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 removed outlier: 4.138A pdb=" N PHE B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 254 through 275 removed outlier: 4.399A pdb=" N ASP B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Proline residue: B 265 - end of helix Processing helix chain 'B' and resid 287 through 305 removed outlier: 3.658A pdb=" N ILE B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 323 through 345 removed outlier: 3.683A pdb=" N LEU B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 368 removed outlier: 4.353A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 416 removed outlier: 3.514A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Proline residue: B 401 - end of helix removed outlier: 4.748A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.523A pdb=" N ASN C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 106 removed outlier: 6.232A pdb=" N ALA C 95 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU C 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 104 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS C 106 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.681A pdb=" N GLU C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.502A pdb=" N ALA C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 228 through 235 removed outlier: 3.667A pdb=" N LEU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 257 removed outlier: 4.503A pdb=" N SER C 257 " --> pdb=" O LYS C 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 257' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 298 removed outlier: 3.560A pdb=" N GLN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 327 through 336 removed outlier: 3.901A pdb=" N ALA C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.890A pdb=" N GLN D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.847A pdb=" N TYR D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 116 removed outlier: 3.640A pdb=" N GLU D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.584A pdb=" N MET D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 152 removed outlier: 3.559A pdb=" N LEU D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 184 removed outlier: 3.789A pdb=" N ALA D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 174 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.644A pdb=" N CYS D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 251 removed outlier: 4.079A pdb=" N PHE D 251 " --> pdb=" O ALA D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'D' and resid 254 through 275 removed outlier: 4.416A pdb=" N ASP D 259 " --> pdb=" O MET D 255 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Proline residue: D 265 - end of helix Processing helix chain 'D' and resid 287 through 305 removed outlier: 3.676A pdb=" N ILE D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ARG D 299 " --> pdb=" O MET D 295 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N PHE D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 323 through 345 removed outlier: 3.703A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 336 " --> pdb=" O PHE D 332 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 368 removed outlier: 4.352A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 416 removed outlier: 3.503A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 392 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 4.751A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 79 removed outlier: 3.522A pdb=" N ASN E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 106 removed outlier: 6.233A pdb=" N ALA E 95 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 98 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 99 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 103 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS E 106 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 133 through 146 removed outlier: 3.681A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'E' and resid 192 through 204 Processing helix chain 'E' and resid 223 through 226 No H-bonds generated for 'chain 'E' and resid 223 through 226' Processing helix chain 'E' and resid 228 through 235 removed outlier: 3.639A pdb=" N LEU E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 removed outlier: 4.503A pdb=" N SER E 257 " --> pdb=" O LYS E 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 254 through 257' Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 280 through 298 removed outlier: 3.561A pdb=" N GLN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 309 Processing helix chain 'E' and resid 327 through 336 removed outlier: 3.901A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 355 Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.889A pdb=" N GLN F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 85 through 94 removed outlier: 3.844A pdb=" N TYR F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 116 removed outlier: 3.637A pdb=" N GLU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 130 removed outlier: 3.582A pdb=" N MET F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 152 removed outlier: 3.532A pdb=" N TRP F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 184 removed outlier: 3.822A pdb=" N ALA F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.774A pdb=" N CYS F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL F 239 " --> pdb=" O PHE F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 251 removed outlier: 4.122A pdb=" N PHE F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 248 through 251' Processing helix chain 'F' and resid 254 through 274 removed outlier: 4.518A pdb=" N ASP F 259 " --> pdb=" O MET F 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 287 through 305 removed outlier: 3.628A pdb=" N ILE F 294 " --> pdb=" O GLN F 290 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE F 297 " --> pdb=" O ARG F 293 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG F 299 " --> pdb=" O MET F 295 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE F 300 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE F 301 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS F 302 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU F 303 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER F 304 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG F 305 " --> pdb=" O PHE F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 318 Processing helix chain 'F' and resid 323 through 345 removed outlier: 3.640A pdb=" N LEU F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 336 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 368 removed outlier: 4.360A pdb=" N TRP F 362 " --> pdb=" O PRO F 358 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP F 363 " --> pdb=" O ASP F 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 365 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 416 removed outlier: 3.566A pdb=" N LEU F 389 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU F 400 " --> pdb=" O LEU F 396 " (cutoff:3.500A) Proline residue: F 401 - end of helix removed outlier: 4.660A pdb=" N VAL F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 405 " --> pdb=" O PRO F 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU F 416 " --> pdb=" O PHE F 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 79 removed outlier: 3.530A pdb=" N ASN G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 105 removed outlier: 6.233A pdb=" N ALA G 95 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL G 98 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU G 99 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE G 103 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS G 104 " --> pdb=" O ASN G 101 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS G 105 " --> pdb=" O ILE G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.681A pdb=" N GLU G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 192 through 204 removed outlier: 3.500A pdb=" N ALA G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 226 No H-bonds generated for 'chain 'G' and resid 223 through 226' Processing helix chain 'G' and resid 228 through 235 removed outlier: 3.666A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 257 removed outlier: 4.499A pdb=" N SER G 257 " --> pdb=" O LYS G 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 254 through 257' Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 280 through 298 removed outlier: 3.521A pdb=" N GLN G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 287 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 309 Processing helix chain 'G' and resid 327 through 336 removed outlier: 3.901A pdb=" N ALA G 336 " --> pdb=" O GLU G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.890A pdb=" N GLN H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.844A pdb=" N TYR H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.638A pdb=" N GLU H 111 " --> pdb=" O ASP H 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 130 removed outlier: 3.583A pdb=" N MET H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 152 removed outlier: 3.513A pdb=" N TRP H 150 " --> pdb=" O GLN H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 184 removed outlier: 3.814A pdb=" N ALA H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU H 174 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR H 184 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.722A pdb=" N CYS H 229 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL H 239 " --> pdb=" O PHE H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 251 removed outlier: 4.186A pdb=" N PHE H 251 " --> pdb=" O ALA H 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 248 through 251' Processing helix chain 'H' and resid 254 through 275 removed outlier: 4.456A pdb=" N ASP H 259 " --> pdb=" O MET H 255 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE H 263 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) Proline residue: H 265 - end of helix Processing helix chain 'H' and resid 287 through 305 removed outlier: 3.654A pdb=" N ILE H 294 " --> pdb=" O GLN H 290 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE H 297 " --> pdb=" O ARG H 293 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU H 298 " --> pdb=" O ILE H 294 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ARG H 299 " --> pdb=" O MET H 295 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE H 300 " --> pdb=" O ARG H 296 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE H 301 " --> pdb=" O ILE H 297 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS H 302 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU H 303 " --> pdb=" O ARG H 299 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N SER H 304 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARG H 305 " --> pdb=" O PHE H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 318 Processing helix chain 'H' and resid 323 through 345 removed outlier: 3.699A pdb=" N LEU H 327 " --> pdb=" O GLU H 323 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA H 345 " --> pdb=" O ALA H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 368 removed outlier: 4.367A pdb=" N TRP H 362 " --> pdb=" O PRO H 358 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP H 363 " --> pdb=" O ASP H 359 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 365 " --> pdb=" O PHE H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 416 removed outlier: 3.576A pdb=" N LEU H 389 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS H 390 " --> pdb=" O VAL H 386 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 391 " --> pdb=" O GLY H 387 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE H 392 " --> pdb=" O SER H 388 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU H 400 " --> pdb=" O LEU H 396 " (cutoff:3.500A) Proline residue: H 401 - end of helix removed outlier: 4.724A pdb=" N VAL H 404 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS H 414 " --> pdb=" O ASN H 410 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU H 416 " --> pdb=" O PHE H 412 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 removed outlier: 7.753A pdb=" N GLY A 53 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 320 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA A 240 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 320 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 242 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 322 " --> pdb=" O THR A 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.633A pdb=" N VAL A 114 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 154 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 156 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR A 184 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA A 157 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY A 186 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS A 212 " --> pdb=" O THR A 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 42 through 47 removed outlier: 3.505A pdb=" N ILE B 37 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 76 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= F, first strand: chain 'C' and resid 52 through 54 removed outlier: 7.755A pdb=" N GLY C 53 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL C 320 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA C 240 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 320 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR C 242 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU C 322 " --> pdb=" O THR C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.633A pdb=" N VAL C 114 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C 154 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE C 156 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 184 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ALA C 157 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY C 186 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS C 212 " --> pdb=" O THR C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 42 through 47 removed outlier: 6.118A pdb=" N TYR D 76 " --> pdb=" O ASN D 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= J, first strand: chain 'E' and resid 52 through 54 removed outlier: 7.755A pdb=" N GLY E 53 " --> pdb=" O SER E 318 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL E 320 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA E 240 " --> pdb=" O SER E 318 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL E 320 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR E 242 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU E 322 " --> pdb=" O THR E 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.635A pdb=" N VAL E 114 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL E 154 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE E 119 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE E 156 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR E 184 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ALA E 157 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY E 186 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS E 212 " --> pdb=" O THR E 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 42 through 47 removed outlier: 6.118A pdb=" N TYR F 76 " --> pdb=" O ASN F 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= N, first strand: chain 'G' and resid 52 through 54 removed outlier: 7.755A pdb=" N GLY G 53 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL G 320 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA G 240 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL G 320 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR G 242 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU G 322 " --> pdb=" O THR G 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 83 through 85 removed outlier: 6.641A pdb=" N VAL G 114 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 154 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE G 119 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE G 156 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ALA G 157 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY G 186 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS G 212 " --> pdb=" O THR G 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 42 through 47 removed outlier: 6.119A pdb=" N TYR H 76 " --> pdb=" O ASN H 38 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2217 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: 6.60 Time building geometry restraints manager: 10.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4463 1.32 - 1.45: 5520 1.45 - 1.57: 12389 1.57 - 1.69: 28 1.69 - 1.81: 200 Bond restraints: 22600 Sorted by residual: bond pdb=" O2B NAP A1001 " pdb=" P2B NAP A1001 " ideal model delta sigma weight residual 1.736 1.612 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O2B NAP G1001 " pdb=" P2B NAP G1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" O2B NAP E1001 " pdb=" P2B NAP E1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" O2B NAP C1001 " pdb=" P2B NAP C1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" O3 NAP A1001 " pdb=" PN NAP A1001 " ideal model delta sigma weight residual 1.643 1.745 -0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 22595 not shown) Histogram of bond angle deviations from ideal: 75.55 - 87.48: 8 87.48 - 99.41: 4 99.41 - 111.34: 9511 111.34 - 123.26: 20167 123.26 - 135.19: 978 Bond angle restraints: 30668 Sorted by residual: angle pdb=" O1A NAP A1001 " pdb=" PA NAP A1001 " pdb=" O3 NAP A1001 " ideal model delta sigma weight residual 111.13 75.55 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" O1A NAP G1001 " pdb=" PA NAP G1001 " pdb=" O3 NAP G1001 " ideal model delta sigma weight residual 111.13 75.58 35.55 3.00e+00 1.11e-01 1.40e+02 angle pdb=" O1A NAP C1001 " pdb=" PA NAP C1001 " pdb=" O3 NAP C1001 " ideal model delta sigma weight residual 111.13 75.62 35.51 3.00e+00 1.11e-01 1.40e+02 angle pdb=" O1A NAP E1001 " pdb=" PA NAP E1001 " pdb=" O3 NAP E1001 " ideal model delta sigma weight residual 111.13 75.65 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C5D NAP E1001 " pdb=" O5D NAP E1001 " pdb=" PN NAP E1001 " ideal model delta sigma weight residual 121.57 100.15 21.42 3.00e+00 1.11e-01 5.10e+01 ... (remaining 30663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 12562 14.89 - 29.78: 712 29.78 - 44.68: 150 44.68 - 59.57: 40 59.57 - 74.46: 16 Dihedral angle restraints: 13480 sinusoidal: 5336 harmonic: 8144 Sorted by residual: dihedral pdb=" CA PHE B 235 " pdb=" C PHE B 235 " pdb=" N GLU B 236 " pdb=" CA GLU B 236 " ideal model delta harmonic sigma weight residual 180.00 155.39 24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA PHE D 235 " pdb=" C PHE D 235 " pdb=" N GLU D 236 " pdb=" CA GLU D 236 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA PRO F 186 " pdb=" C PRO F 186 " pdb=" N ILE F 187 " pdb=" CA ILE F 187 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 13477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 3332 0.153 - 0.306: 64 0.306 - 0.459: 16 0.459 - 0.612: 0 0.612 - 0.765: 4 Chirality restraints: 3416 Sorted by residual: chirality pdb=" C2B NAP E1001 " pdb=" C1B NAP E1001 " pdb=" C3B NAP E1001 " pdb=" O2B NAP E1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" C2B NAP C1001 " pdb=" C1B NAP C1001 " pdb=" C3B NAP C1001 " pdb=" O2B NAP C1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C2B NAP A1001 " pdb=" C1B NAP A1001 " pdb=" C3B NAP A1001 " pdb=" O2B NAP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 3413 not shown) Planarity restraints: 3892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 103 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ILE G 103 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE G 103 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS G 104 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 136 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C ILE C 136 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE C 136 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 137 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 294 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" C ILE D 294 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE D 294 " -0.018 2.00e-02 2.50e+03 pdb=" N MET D 295 " -0.016 2.00e-02 2.50e+03 ... (remaining 3889 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 312 2.62 - 3.19: 19708 3.19 - 3.76: 34621 3.76 - 4.33: 51209 4.33 - 4.90: 80144 Nonbonded interactions: 185994 Sorted by model distance: nonbonded pdb=" OD1 ASP B 375 " pdb=" N MET B 376 " model vdw 2.049 2.520 nonbonded pdb=" OD1 ASP D 375 " pdb=" N MET D 376 " model vdw 2.051 2.520 nonbonded pdb=" OD1 ASP F 375 " pdb=" N MET F 376 " model vdw 2.053 2.520 nonbonded pdb=" OD1 ASP H 375 " pdb=" N MET H 376 " model vdw 2.054 2.520 nonbonded pdb=" NH2 ARG B 34 " pdb=" OE1 GLU B 45 " model vdw 2.072 2.520 ... (remaining 185989 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 0.010 Normalize map: mean=0, sd=1: 3.590 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: 12.690 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 62.890 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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 : 0.012 0.124 22600 Z= 0.750 Angle : 1.291 35.578 30668 Z= 0.656 Chirality : 0.070 0.765 3416 Planarity : 0.008 0.068 3892 Dihedral : 10.861 74.461 8272 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 0.13 % Allowed : 1.53 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.12), residues: 2832 helix: -3.55 (0.08), residues: 1608 sheet: -0.54 (0.38), residues: 176 loop : -2.39 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 185 HIS 0.012 0.004 HIS F 306 PHE 0.031 0.004 PHE E 84 TYR 0.045 0.004 TYR H 116 ARG 0.022 0.002 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 723 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 726 average time/residue: 0.3793 time to fit residues: 408.7756 Evaluate side-chains 487 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 485 time to evaluate : 2.594 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1945 time to fit residues: 4.1963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 113 optimal weight: 30.0000 chunk 219 optimal weight: 0.5980 chunk 84 optimal weight: 0.2980 chunk 133 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 135 HIS A 175 HIS A 314 ASN A 333 ASN B 53 GLN B 353 GLN B 414 HIS C 135 HIS C 175 HIS C 204 GLN C 271 GLN C 314 ASN D 53 GLN D 81 ASN D 353 GLN D 414 HIS E 135 HIS E 175 HIS E 271 GLN E 314 ASN F 53 GLN F 353 GLN F 414 HIS G 79 ASN G 135 HIS G 175 HIS G 204 GLN G 271 GLN G 314 ASN H 53 GLN H 290 GLN H 353 GLN H 414 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22600 Z= 0.208 Angle : 0.670 11.055 30668 Z= 0.337 Chirality : 0.044 0.245 3416 Planarity : 0.005 0.043 3892 Dihedral : 8.911 62.673 3360 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.88 % Allowed : 9.62 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.64 (0.14), residues: 2832 helix: -1.76 (0.11), residues: 1584 sheet: -0.43 (0.39), residues: 176 loop : -1.72 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 232 HIS 0.003 0.001 HIS C 135 PHE 0.029 0.002 PHE F 361 TYR 0.016 0.002 TYR H 90 ARG 0.004 0.000 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 533 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 34 residues processed: 561 average time/residue: 0.3660 time to fit residues: 309.2746 Evaluate side-chains 493 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 459 time to evaluate : 2.589 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2465 time to fit residues: 18.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 226 optimal weight: 0.8980 chunk 252 optimal weight: 0.0870 chunk 86 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 286 GLN B 53 GLN C 286 GLN C 333 ASN D 81 ASN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 286 GLN E 333 ASN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 GLN G 333 ASN H 53 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22600 Z= 0.362 Angle : 0.714 12.591 30668 Z= 0.348 Chirality : 0.046 0.249 3416 Planarity : 0.005 0.051 3892 Dihedral : 8.496 59.473 3360 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.66 % Allowed : 12.77 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.81 (0.15), residues: 2832 helix: -1.02 (0.12), residues: 1600 sheet: -0.05 (0.46), residues: 136 loop : -1.43 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 150 HIS 0.010 0.001 HIS C 135 PHE 0.033 0.002 PHE H 361 TYR 0.018 0.002 TYR B 76 ARG 0.004 0.001 ARG G 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 491 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 504 average time/residue: 0.3577 time to fit residues: 274.7245 Evaluate side-chains 474 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 450 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2390 time to fit residues: 14.1844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 1.9990 chunk 191 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 255 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN H 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22600 Z= 0.349 Angle : 0.704 14.335 30668 Z= 0.339 Chirality : 0.046 0.229 3416 Planarity : 0.005 0.045 3892 Dihedral : 7.940 61.273 3360 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.44 % Allowed : 14.30 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 2832 helix: -0.58 (0.13), residues: 1552 sheet: -0.30 (0.46), residues: 136 loop : -1.21 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 232 HIS 0.009 0.001 HIS A 135 PHE 0.041 0.002 PHE D 237 TYR 0.016 0.002 TYR B 116 ARG 0.005 0.000 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 470 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 487 average time/residue: 0.3577 time to fit residues: 267.2190 Evaluate side-chains 455 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 437 time to evaluate : 2.512 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1972 time to fit residues: 9.9503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22600 Z= 0.288 Angle : 0.676 11.768 30668 Z= 0.325 Chirality : 0.045 0.210 3416 Planarity : 0.004 0.044 3892 Dihedral : 7.201 56.588 3360 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.90 % Allowed : 16.10 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2832 helix: -0.28 (0.13), residues: 1544 sheet: -0.34 (0.47), residues: 136 loop : -1.07 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 232 HIS 0.008 0.001 HIS G 135 PHE 0.044 0.002 PHE D 237 TYR 0.012 0.001 TYR B 116 ARG 0.007 0.000 ARG F 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 452 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 461 average time/residue: 0.3718 time to fit residues: 263.1587 Evaluate side-chains 433 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 424 time to evaluate : 2.555 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2050 time to fit residues: 6.7248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 224 optimal weight: 0.7980 chunk 125 optimal weight: 0.1980 chunk 22 optimal weight: 0.0670 chunk 89 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22600 Z= 0.154 Angle : 0.622 10.895 30668 Z= 0.300 Chirality : 0.042 0.181 3416 Planarity : 0.004 0.045 3892 Dihedral : 6.561 54.858 3360 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.72 % Allowed : 16.14 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2832 helix: -0.13 (0.13), residues: 1552 sheet: 0.28 (0.44), residues: 156 loop : -0.90 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 363 HIS 0.004 0.001 HIS E 135 PHE 0.029 0.001 PHE D 237 TYR 0.010 0.001 TYR E 255 ARG 0.006 0.000 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 466 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 476 average time/residue: 0.3558 time to fit residues: 260.1382 Evaluate side-chains 434 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 429 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2063 time to fit residues: 5.3129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 197 optimal weight: 50.0000 chunk 153 optimal weight: 0.6980 chunk 228 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 269 optimal weight: 30.0000 chunk 168 optimal weight: 3.9990 chunk 164 optimal weight: 0.0270 chunk 124 optimal weight: 5.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS C 349 HIS D 315 GLN F 315 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22600 Z= 0.264 Angle : 0.669 11.505 30668 Z= 0.324 Chirality : 0.044 0.188 3416 Planarity : 0.004 0.047 3892 Dihedral : 6.242 52.690 3360 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.81 % Allowed : 16.95 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2832 helix: -0.08 (0.13), residues: 1548 sheet: -0.54 (0.37), residues: 216 loop : -0.74 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 362 HIS 0.008 0.001 HIS C 135 PHE 0.049 0.002 PHE D 237 TYR 0.009 0.001 TYR B 116 ARG 0.007 0.000 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 444 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 448 average time/residue: 0.3545 time to fit residues: 243.1978 Evaluate side-chains 436 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 430 time to evaluate : 2.597 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2061 time to fit residues: 5.6486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 53 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 50.0000 chunk 133 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 212 optimal weight: 0.3980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN F 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22600 Z= 0.180 Angle : 0.667 11.507 30668 Z= 0.322 Chirality : 0.043 0.190 3416 Planarity : 0.004 0.049 3892 Dihedral : 6.056 53.210 3360 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.36 % Allowed : 17.85 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.16), residues: 2832 helix: 0.03 (0.13), residues: 1544 sheet: -0.49 (0.37), residues: 216 loop : -0.63 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 362 HIS 0.005 0.001 HIS C 135 PHE 0.056 0.002 PHE F 330 TYR 0.009 0.001 TYR F 266 ARG 0.008 0.000 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 442 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 445 average time/residue: 0.3547 time to fit residues: 242.0828 Evaluate side-chains 440 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 437 time to evaluate : 2.662 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2239 time to fit residues: 4.9324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 0.4980 chunk 258 optimal weight: 50.0000 chunk 235 optimal weight: 0.9990 chunk 251 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 221 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22600 Z= 0.191 Angle : 0.681 14.388 30668 Z= 0.329 Chirality : 0.043 0.195 3416 Planarity : 0.004 0.050 3892 Dihedral : 5.981 52.815 3360 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.18 % Allowed : 18.21 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2832 helix: 0.07 (0.13), residues: 1544 sheet: -0.47 (0.37), residues: 216 loop : -0.55 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 362 HIS 0.006 0.001 HIS C 135 PHE 0.051 0.002 PHE D 237 TYR 0.012 0.001 TYR H 343 ARG 0.009 0.000 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 443 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 445 average time/residue: 0.3737 time to fit residues: 257.0938 Evaluate side-chains 433 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 431 time to evaluate : 2.477 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2489 time to fit residues: 4.4040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.8980 chunk 265 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 126 optimal weight: 50.0000 chunk 184 optimal weight: 40.0000 chunk 278 optimal weight: 9.9990 chunk 256 optimal weight: 2.9990 chunk 222 optimal weight: 0.0870 chunk 23 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22600 Z= 0.352 Angle : 0.740 13.617 30668 Z= 0.362 Chirality : 0.046 0.217 3416 Planarity : 0.004 0.049 3892 Dihedral : 6.290 53.592 3360 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.27 % Allowed : 18.35 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2832 helix: -0.01 (0.13), residues: 1556 sheet: -0.81 (0.40), residues: 176 loop : -0.57 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 362 HIS 0.008 0.001 HIS C 135 PHE 0.059 0.002 PHE H 330 TYR 0.015 0.001 TYR B 116 ARG 0.008 0.000 ARG C 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 443 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 444 average time/residue: 0.3563 time to fit residues: 242.7536 Evaluate side-chains 432 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 429 time to evaluate : 2.643 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2134 time to fit residues: 4.7057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 32 optimal weight: 0.0970 chunk 61 optimal weight: 9.9990 chunk 222 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.195706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150790 restraints weight = 29330.703| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.10 r_work: 0.3134 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22600 Z= 0.211 Angle : 0.716 13.174 30668 Z= 0.347 Chirality : 0.044 0.245 3416 Planarity : 0.004 0.049 3892 Dihedral : 6.073 53.683 3360 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.13 % Allowed : 18.44 % Favored : 81.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2832 helix: 0.06 (0.13), residues: 1548 sheet: -0.54 (0.37), residues: 216 loop : -0.51 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 362 HIS 0.006 0.001 HIS C 135 PHE 0.056 0.002 PHE B 361 TYR 0.010 0.001 TYR H 343 ARG 0.008 0.000 ARG G 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6346.94 seconds wall clock time: 114 minutes 9.52 seconds (6849.52 seconds total)