Starting phenix.real_space_refine (version: dev) on Thu Dec 22 12:16:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/12_2022/7u67_26362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/12_2022/7u67_26362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/12_2022/7u67_26362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/12_2022/7u67_26362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/12_2022/7u67_26362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/12_2022/7u67_26362_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22158 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 35": "OD1" <-> "OD2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "J ASP 33": "OD1" <-> "OD2" Residue "I ASP 33": "OD1" <-> "OD2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "L ASP 33": "OD1" <-> "OD2" Residue "K ASP 33": "OD1" <-> "OD2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 483": "OD1" <-> "OD2" Residue "D TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ASP 268": "OD1" <-> "OD2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 483": "OD1" <-> "OD2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 35": "OD1" <-> "OD2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ASP 268": "OD1" <-> "OD2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 483": "OD1" <-> "OD2" Residue "F TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E ASP 268": "OD1" <-> "OD2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 483": "OD1" <-> "OD2" Residue "E TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 26778 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3733 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 454} Chain breaks: 6 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "G" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 697 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 697 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 697 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 697 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 697 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 697 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3733 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 454} Chain breaks: 6 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "C" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3733 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 454} Chain breaks: 6 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "B" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3733 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 454} Chain breaks: 6 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "F" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3733 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 454} Chain breaks: 6 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "E" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3733 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 454} Chain breaks: 6 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.59, per 1000 atoms: 0.54 Number of scatterers: 26778 At special positions: 0 Unit cell: (132.344, 138.868, 138.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 18 15.00 Mg 6 11.99 O 4698 8.00 N 4674 7.00 C 17262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 3.8 seconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 6 sheets defined 60.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 25 through 40 removed outlier: 3.565A pdb=" N LEU A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.917A pdb=" N LEU A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 90 removed outlier: 3.528A pdb=" N GLU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.919A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.720A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 167 through 181 removed outlier: 3.810A pdb=" N GLU A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.611A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 4.133A pdb=" N ILE A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 237 through 250 removed outlier: 5.198A pdb=" N ALA A 241 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 removed outlier: 3.626A pdb=" N TRP A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 333 through 354 removed outlier: 4.005A pdb=" N VAL A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.718A pdb=" N LEU A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 419 removed outlier: 3.585A pdb=" N LEU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.831A pdb=" N LYS A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'A' and resid 469 through 486 removed outlier: 3.529A pdb=" N ILE A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'G' and resid 6 through 22 removed outlier: 4.214A pdb=" N LEU G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 83 Processing helix chain 'J' and resid 6 through 22 removed outlier: 4.214A pdb=" N LEU J 22 " --> pdb=" O LYS J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 83 Processing helix chain 'I' and resid 6 through 22 removed outlier: 4.213A pdb=" N LEU I 22 " --> pdb=" O LYS I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 83 Processing helix chain 'H' and resid 6 through 22 removed outlier: 4.214A pdb=" N LEU H 22 " --> pdb=" O LYS H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 83 Processing helix chain 'L' and resid 6 through 22 removed outlier: 4.214A pdb=" N LEU L 22 " --> pdb=" O LYS L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 83 Processing helix chain 'K' and resid 6 through 22 removed outlier: 4.213A pdb=" N LEU K 22 " --> pdb=" O LYS K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 83 Processing helix chain 'D' and resid 6 through 8 No H-bonds generated for 'chain 'D' and resid 6 through 8' Processing helix chain 'D' and resid 25 through 40 removed outlier: 3.564A pdb=" N LEU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 35 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG D 36 " --> pdb=" O PHE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 removed outlier: 3.917A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 90 removed outlier: 3.529A pdb=" N GLU D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.919A pdb=" N GLU D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 110 " --> pdb=" O PHE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 140 removed outlier: 3.721A pdb=" N ILE D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG D 139 " --> pdb=" O TRP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 167 through 181 removed outlier: 3.811A pdb=" N GLU D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU D 172 " --> pdb=" O PRO D 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 removed outlier: 3.611A pdb=" N ILE D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 removed outlier: 4.133A pdb=" N ILE D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 237 through 250 removed outlier: 5.198A pdb=" N ALA D 241 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 244 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 270 removed outlier: 3.626A pdb=" N TRP D 262 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 288 through 299 Processing helix chain 'D' and resid 312 through 318 Processing helix chain 'D' and resid 333 through 354 removed outlier: 4.005A pdb=" N VAL D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Proline residue: D 346 - end of helix Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.718A pdb=" N LEU D 379 " --> pdb=" O CYS D 375 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 380 " --> pdb=" O SER D 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 419 removed outlier: 3.584A pdb=" N LEU D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Proline residue: D 416 - end of helix Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.832A pdb=" N LYS D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 459 Processing helix chain 'D' and resid 469 through 486 removed outlier: 3.529A pdb=" N ILE D 485 " --> pdb=" O LEU D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 500 Processing helix chain 'C' and resid 6 through 8 No H-bonds generated for 'chain 'C' and resid 6 through 8' Processing helix chain 'C' and resid 25 through 40 removed outlier: 3.565A pdb=" N LEU C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 removed outlier: 3.916A pdb=" N LEU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 90 removed outlier: 3.528A pdb=" N GLU C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.919A pdb=" N GLU C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 140 removed outlier: 3.720A pdb=" N ILE C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 139 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 167 through 181 removed outlier: 3.811A pdb=" N GLU C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 removed outlier: 3.611A pdb=" N ILE C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 209 removed outlier: 4.133A pdb=" N ILE C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 237 through 250 removed outlier: 5.198A pdb=" N ALA C 241 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 244 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 270 removed outlier: 3.626A pdb=" N TRP C 262 " --> pdb=" O PRO C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 288 through 299 Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 333 through 354 removed outlier: 4.005A pdb=" N VAL C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Proline residue: C 346 - end of helix Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 374 through 389 removed outlier: 3.719A pdb=" N LEU C 379 " --> pdb=" O CYS C 375 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 381 " --> pdb=" O ASP C 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 419 removed outlier: 3.584A pdb=" N LEU C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Proline residue: C 416 - end of helix Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.831A pdb=" N LYS C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 459 Processing helix chain 'C' and resid 469 through 486 removed outlier: 3.529A pdb=" N ILE C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 500 Processing helix chain 'B' and resid 6 through 8 No H-bonds generated for 'chain 'B' and resid 6 through 8' Processing helix chain 'B' and resid 25 through 40 removed outlier: 3.564A pdb=" N LEU B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 36 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 removed outlier: 3.917A pdb=" N LEU B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 90 removed outlier: 3.528A pdb=" N GLU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.919A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 removed outlier: 3.720A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 139 " --> pdb=" O TRP B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.810A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 removed outlier: 3.611A pdb=" N ILE B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 4.133A pdb=" N ILE B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 237 through 250 removed outlier: 5.197A pdb=" N ALA B 241 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 244 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.627A pdb=" N TRP B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 288 through 299 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 333 through 354 removed outlier: 4.005A pdb=" N VAL B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.717A pdb=" N LEU B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 381 " --> pdb=" O ASP B 377 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 419 removed outlier: 3.585A pdb=" N LEU B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Proline residue: B 416 - end of helix Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.830A pdb=" N LYS B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 459 Processing helix chain 'B' and resid 469 through 486 removed outlier: 3.529A pdb=" N ILE B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 500 Processing helix chain 'F' and resid 6 through 8 No H-bonds generated for 'chain 'F' and resid 6 through 8' Processing helix chain 'F' and resid 25 through 40 removed outlier: 3.565A pdb=" N LEU F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE F 32 " --> pdb=" O ILE F 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 50 removed outlier: 3.916A pdb=" N LEU F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLN F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN F 50 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 90 removed outlier: 3.528A pdb=" N GLU F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.919A pdb=" N GLU F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 140 removed outlier: 3.721A pdb=" N ILE F 132 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG F 139 " --> pdb=" O TRP F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 167 through 181 removed outlier: 3.811A pdb=" N GLU F 171 " --> pdb=" O GLU F 167 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU F 172 " --> pdb=" O PRO F 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS F 181 " --> pdb=" O ARG F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 194 removed outlier: 3.612A pdb=" N ILE F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 209 removed outlier: 4.133A pdb=" N ILE F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 237 through 250 removed outlier: 5.198A pdb=" N ALA F 241 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 244 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 270 removed outlier: 3.627A pdb=" N TRP F 262 " --> pdb=" O PRO F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 288 through 299 Processing helix chain 'F' and resid 312 through 318 Processing helix chain 'F' and resid 333 through 354 removed outlier: 4.004A pdb=" N VAL F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) Proline residue: F 346 - end of helix Processing helix chain 'F' and resid 356 through 361 Processing helix chain 'F' and resid 374 through 389 removed outlier: 3.718A pdb=" N LEU F 379 " --> pdb=" O CYS F 375 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 380 " --> pdb=" O SER F 376 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 381 " --> pdb=" O ASP F 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 419 removed outlier: 3.585A pdb=" N LEU F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU F 400 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Proline residue: F 416 - end of helix Processing helix chain 'F' and resid 422 through 431 Processing helix chain 'F' and resid 438 through 446 removed outlier: 3.831A pdb=" N LYS F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 459 Processing helix chain 'F' and resid 469 through 486 removed outlier: 3.529A pdb=" N ILE F 485 " --> pdb=" O LEU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 500 Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 25 through 40 removed outlier: 3.565A pdb=" N LEU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG E 36 " --> pdb=" O PHE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 removed outlier: 3.917A pdb=" N LEU E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 90 removed outlier: 3.528A pdb=" N GLU E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 115 removed outlier: 3.919A pdb=" N GLU E 107 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 140 removed outlier: 3.720A pdb=" N ILE E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG E 139 " --> pdb=" O TRP E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 167 through 181 removed outlier: 3.811A pdb=" N GLU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU E 172 " --> pdb=" O PRO E 168 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 194 removed outlier: 3.611A pdb=" N ILE E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 209 removed outlier: 4.133A pdb=" N ILE E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 237 through 250 removed outlier: 5.198A pdb=" N ALA E 241 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 244 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 270 removed outlier: 3.626A pdb=" N TRP E 262 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 288 through 299 Processing helix chain 'E' and resid 312 through 318 Processing helix chain 'E' and resid 333 through 354 removed outlier: 4.004A pdb=" N VAL E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Proline residue: E 346 - end of helix Processing helix chain 'E' and resid 356 through 361 Processing helix chain 'E' and resid 374 through 389 removed outlier: 3.718A pdb=" N LEU E 379 " --> pdb=" O CYS E 375 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 380 " --> pdb=" O SER E 376 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 381 " --> pdb=" O ASP E 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 419 removed outlier: 3.585A pdb=" N LEU E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Proline residue: E 416 - end of helix Processing helix chain 'E' and resid 422 through 431 Processing helix chain 'E' and resid 438 through 446 removed outlier: 3.830A pdb=" N LYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 459 Processing helix chain 'E' and resid 469 through 486 removed outlier: 3.530A pdb=" N ILE E 485 " --> pdb=" O LEU E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 500 Processing sheet with id= A, first strand: chain 'G' and resid 24 through 32 removed outlier: 6.789A pdb=" N ASP G 47 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU G 52 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 24 through 32 removed outlier: 6.789A pdb=" N ASP J 47 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU J 52 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 24 through 32 removed outlier: 6.788A pdb=" N ASP I 47 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU I 52 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 24 through 32 removed outlier: 6.789A pdb=" N ASP H 47 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU H 52 " --> pdb=" O ASP H 47 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 24 through 32 removed outlier: 6.789A pdb=" N ASP L 47 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU L 52 " --> pdb=" O ASP L 47 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 24 through 32 removed outlier: 6.789A pdb=" N ASP K 47 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU K 52 " --> pdb=" O ASP K 47 " (cutoff:3.500A) 1278 hydrogen bonds defined for protein. 3510 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: 7.25 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4225 1.31 - 1.44: 7992 1.44 - 1.56: 15017 1.56 - 1.68: 30 1.68 - 1.81: 192 Bond restraints: 27456 Sorted by residual: bond pdb=" C LEU C 140 " pdb=" O LEU C 140 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" C LEU E 140 " pdb=" O LEU E 140 " ideal model delta sigma weight residual 1.235 1.190 0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" C LEU A 140 " pdb=" O LEU A 140 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.25e-02 6.40e+03 1.25e+01 bond pdb=" C LEU B 140 " pdb=" O LEU B 140 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.25e-02 6.40e+03 1.25e+01 bond pdb=" C LEU F 140 " pdb=" O LEU F 140 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.25e-02 6.40e+03 1.23e+01 ... (remaining 27451 not shown) Histogram of bond angle deviations from ideal: 100.27 - 108.14: 1234 108.14 - 116.01: 16324 116.01 - 123.87: 18933 123.87 - 131.74: 775 131.74 - 139.61: 90 Bond angle restraints: 37356 Sorted by residual: angle pdb=" PB GTP A 601 " pdb=" O3B GTP A 601 " pdb=" PG GTP A 601 " ideal model delta sigma weight residual 120.50 139.61 -19.11 3.00e+00 1.11e-01 4.06e+01 angle pdb=" PB GTP D 601 " pdb=" O3B GTP D 601 " pdb=" PG GTP D 601 " ideal model delta sigma weight residual 120.50 139.60 -19.10 3.00e+00 1.11e-01 4.05e+01 angle pdb=" PB GTP C 601 " pdb=" O3B GTP C 601 " pdb=" PG GTP C 601 " ideal model delta sigma weight residual 120.50 139.60 -19.10 3.00e+00 1.11e-01 4.05e+01 angle pdb=" PB GTP F 601 " pdb=" O3B GTP F 601 " pdb=" PG GTP F 601 " ideal model delta sigma weight residual 120.50 139.59 -19.09 3.00e+00 1.11e-01 4.05e+01 angle pdb=" PB GTP E 601 " pdb=" O3B GTP E 601 " pdb=" PG GTP E 601 " ideal model delta sigma weight residual 120.50 139.58 -19.08 3.00e+00 1.11e-01 4.04e+01 ... (remaining 37351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 15498 33.32 - 66.64: 552 66.64 - 99.96: 30 99.96 - 133.28: 12 133.28 - 166.59: 18 Dihedral angle restraints: 16110 sinusoidal: 6168 harmonic: 9942 Sorted by residual: dihedral pdb=" C8 GTP F 601 " pdb=" C1' GTP F 601 " pdb=" N9 GTP F 601 " pdb=" O4' GTP F 601 " ideal model delta sinusoidal sigma weight residual 104.59 -62.00 166.59 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP D 601 " pdb=" C1' GTP D 601 " pdb=" N9 GTP D 601 " pdb=" O4' GTP D 601 " ideal model delta sinusoidal sigma weight residual 104.59 -62.00 166.59 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP B 601 " pdb=" C1' GTP B 601 " pdb=" N9 GTP B 601 " pdb=" O4' GTP B 601 " ideal model delta sinusoidal sigma weight residual 104.59 -61.97 166.57 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 16107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3622 0.058 - 0.117: 416 0.117 - 0.175: 39 0.175 - 0.234: 45 0.234 - 0.292: 18 Chirality restraints: 4140 Sorted by residual: chirality pdb=" CA ARG C 415 " pdb=" N ARG C 415 " pdb=" C ARG C 415 " pdb=" CB ARG C 415 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ARG E 415 " pdb=" N ARG E 415 " pdb=" C ARG E 415 " pdb=" CB ARG E 415 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ARG F 415 " pdb=" N ARG F 415 " pdb=" C ARG F 415 " pdb=" CB ARG F 415 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4137 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 77 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C GLY C 77 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY C 77 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 78 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 77 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C GLY E 77 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY E 77 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG E 78 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 77 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C GLY B 77 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY B 77 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 78 " -0.014 2.00e-02 2.50e+03 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 583 2.71 - 3.26: 25249 3.26 - 3.80: 40937 3.80 - 4.35: 53852 4.35 - 4.90: 90885 Nonbonded interactions: 211506 Sorted by model distance: nonbonded pdb=" NE2 HIS B 117 " pdb="MG MG B 602 " model vdw 2.161 2.250 nonbonded pdb=" NE2 HIS F 117 " pdb="MG MG F 602 " model vdw 2.162 2.250 nonbonded pdb=" NE2 HIS A 117 " pdb="MG MG A 602 " model vdw 2.162 2.250 nonbonded pdb=" NE2 HIS C 117 " pdb="MG MG C 602 " model vdw 2.162 2.250 nonbonded pdb=" NE2 HIS D 117 " pdb="MG MG D 602 " model vdw 2.162 2.250 ... (remaining 211501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 120 5.16 5 C 17262 2.51 5 N 4674 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.020 Extract box with map and model: 5.270 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.220 Process input model: 62.780 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.005 0.057 27456 Z= 0.342 Angle : 0.748 19.105 37356 Z= 0.389 Chirality : 0.047 0.292 4140 Planarity : 0.004 0.040 4668 Dihedral : 17.774 166.595 9654 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.91 % 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: -0.22 (0.15), residues: 3264 helix: 0.03 (0.11), residues: 2148 sheet: 1.62 (0.42), residues: 162 loop : -0.55 (0.20), residues: 954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 563 time to evaluate : 2.902 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 575 average time/residue: 1.6784 time to fit residues: 1085.4664 Evaluate side-chains 531 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 522 time to evaluate : 2.749 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.3840 time to fit residues: 5.7076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.0980 chunk 250 optimal weight: 3.9990 chunk 138 optimal weight: 0.0470 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS D 69 HIS D 384 ASN D 445 HIS C 69 HIS B 69 HIS B 251 ASN F 69 HIS E 69 HIS E 251 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 27456 Z= 0.160 Angle : 0.513 9.119 37356 Z= 0.257 Chirality : 0.038 0.117 4140 Planarity : 0.004 0.038 4668 Dihedral : 11.664 170.761 3792 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.25 % 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: 0.68 (0.15), residues: 3264 helix: 0.91 (0.11), residues: 2154 sheet: 1.64 (0.43), residues: 162 loop : -0.68 (0.20), residues: 948 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 529 time to evaluate : 2.972 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 14 residues processed: 560 average time/residue: 1.6160 time to fit residues: 1024.9844 Evaluate side-chains 539 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 525 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.4775 time to fit residues: 9.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 249 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 82 optimal weight: 0.0170 chunk 300 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 297 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN D 445 HIS B 251 ASN E 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 27456 Z= 0.230 Angle : 0.521 6.830 37356 Z= 0.262 Chirality : 0.039 0.130 4140 Planarity : 0.004 0.039 4668 Dihedral : 11.346 179.907 3792 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 2.55 % 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: 0.78 (0.15), residues: 3264 helix: 1.06 (0.11), residues: 2148 sheet: 1.63 (0.40), residues: 162 loop : -0.82 (0.20), residues: 954 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 516 time to evaluate : 3.278 Fit side-chains outliers start: 67 outliers final: 24 residues processed: 545 average time/residue: 1.6366 time to fit residues: 1008.1680 Evaluate side-chains 541 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 517 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 10 residues processed: 14 average time/residue: 0.2860 time to fit residues: 11.1452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 chunk 318 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 445 HIS B 251 ASN E 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 27456 Z= 0.367 Angle : 0.587 6.777 37356 Z= 0.297 Chirality : 0.043 0.143 4140 Planarity : 0.005 0.040 4668 Dihedral : 11.220 177.641 3792 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.15), residues: 3264 helix: 0.87 (0.11), residues: 2160 sheet: 1.45 (0.39), residues: 162 loop : -0.98 (0.20), residues: 942 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 523 time to evaluate : 3.159 Fit side-chains outliers start: 91 outliers final: 46 residues processed: 576 average time/residue: 1.7044 time to fit residues: 1112.5604 Evaluate side-chains 560 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 514 time to evaluate : 3.007 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 30 residues processed: 16 average time/residue: 0.4122 time to fit residues: 14.1387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 237 optimal weight: 0.0170 chunk 131 optimal weight: 5.9990 chunk 272 optimal weight: 0.0870 chunk 220 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 286 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS D 11 ASN D 445 HIS C 41 ASN F 13 HIS F 74 GLN E 445 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 27456 Z= 0.117 Angle : 0.450 6.447 37356 Z= 0.226 Chirality : 0.036 0.166 4140 Planarity : 0.004 0.041 4668 Dihedral : 10.751 174.533 3792 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 2.89 % 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: 1.00 (0.15), residues: 3264 helix: 1.24 (0.12), residues: 2160 sheet: 1.45 (0.39), residues: 162 loop : -0.75 (0.20), residues: 942 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 516 time to evaluate : 3.277 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 39 residues processed: 570 average time/residue: 1.5921 time to fit residues: 1029.6665 Evaluate side-chains 553 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 514 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 30 residues processed: 9 average time/residue: 0.6404 time to fit residues: 11.7158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 319 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN D 365 ASN D 445 HIS B 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 27456 Z= 0.438 Angle : 0.615 7.023 37356 Z= 0.311 Chirality : 0.045 0.148 4140 Planarity : 0.005 0.043 4668 Dihedral : 10.926 179.598 3792 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 3.23 % 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: 0.57 (0.15), residues: 3264 helix: 0.92 (0.11), residues: 2160 sheet: 1.40 (0.40), residues: 162 loop : -0.97 (0.20), residues: 942 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 521 time to evaluate : 3.117 Fit side-chains outliers start: 85 outliers final: 49 residues processed: 572 average time/residue: 1.6402 time to fit residues: 1066.2248 Evaluate side-chains 565 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 516 time to evaluate : 3.055 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 36 residues processed: 13 average time/residue: 0.4457 time to fit residues: 13.0246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 193 optimal weight: 0.0770 chunk 146 optimal weight: 0.0570 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 445 HIS B 178 GLN B 342 ASN B 384 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 27456 Z= 0.135 Angle : 0.470 7.772 37356 Z= 0.237 Chirality : 0.037 0.153 4140 Planarity : 0.004 0.040 4668 Dihedral : 10.631 175.672 3792 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 2.36 % 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: 0.97 (0.15), residues: 3264 helix: 1.24 (0.12), residues: 2154 sheet: 1.39 (0.41), residues: 162 loop : -0.79 (0.20), residues: 948 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 512 time to evaluate : 3.027 Fit side-chains outliers start: 62 outliers final: 38 residues processed: 555 average time/residue: 1.6306 time to fit residues: 1024.6129 Evaluate side-chains 545 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 507 time to evaluate : 3.275 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 7 average time/residue: 0.9197 time to fit residues: 12.1331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 445 HIS ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 27456 Z= 0.418 Angle : 0.614 18.525 37356 Z= 0.309 Chirality : 0.045 0.229 4140 Planarity : 0.005 0.040 4668 Dihedral : 10.845 179.787 3792 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 2.51 % 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: 0.56 (0.15), residues: 3264 helix: 0.91 (0.11), residues: 2160 sheet: 1.37 (0.41), residues: 162 loop : -0.96 (0.20), residues: 942 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 522 time to evaluate : 3.549 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 47 residues processed: 565 average time/residue: 1.6603 time to fit residues: 1065.3399 Evaluate side-chains 561 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 514 time to evaluate : 3.018 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 33 residues processed: 14 average time/residue: 0.5115 time to fit residues: 14.3331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.7980 chunk 304 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 232 optimal weight: 0.0670 chunk 90 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 280 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN D 178 GLN D 365 ASN D 445 HIS B 13 HIS B 342 ASN F 74 GLN E 294 HIS E 445 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.074 27456 Z= 0.156 Angle : 0.502 14.868 37356 Z= 0.252 Chirality : 0.038 0.166 4140 Planarity : 0.004 0.040 4668 Dihedral : 10.648 177.976 3792 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.75 % 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: 0.89 (0.15), residues: 3264 helix: 1.15 (0.12), residues: 2166 sheet: 1.27 (0.41), residues: 162 loop : -0.76 (0.21), residues: 936 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 518 time to evaluate : 3.394 Fit side-chains outliers start: 46 outliers final: 36 residues processed: 549 average time/residue: 1.6695 time to fit residues: 1036.7909 Evaluate side-chains 552 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 516 time to evaluate : 2.977 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 7 average time/residue: 0.4089 time to fit residues: 8.5204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 0.9990 chunk 313 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 302 optimal weight: 0.2980 chunk 261 optimal weight: 4.9990 chunk 27 optimal weight: 0.0270 chunk 202 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 445 HIS B 342 ASN E 294 HIS E 445 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 27456 Z= 0.157 Angle : 0.498 9.783 37356 Z= 0.250 Chirality : 0.038 0.256 4140 Planarity : 0.004 0.039 4668 Dihedral : 10.536 177.000 3792 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.41 % 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: 0.98 (0.15), residues: 3264 helix: 1.21 (0.12), residues: 2166 sheet: 1.19 (0.40), residues: 162 loop : -0.64 (0.21), residues: 936 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 515 time to evaluate : 2.793 Fit side-chains outliers start: 37 outliers final: 32 residues processed: 546 average time/residue: 1.6823 time to fit residues: 1042.3304 Evaluate side-chains 543 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 511 time to evaluate : 3.024 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 3 average time/residue: 1.0688 time to fit residues: 7.9273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 445 HIS B 178 GLN B 342 ASN E 290 GLN E 294 HIS E 445 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116578 restraints weight = 33633.904| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.37 r_work: 0.3424 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 27456 Z= 0.241 Angle : 0.542 10.559 37356 Z= 0.275 Chirality : 0.040 0.263 4140 Planarity : 0.004 0.038 4668 Dihedral : 10.601 178.903 3792 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3264 helix: 1.15 (0.12), residues: 2160 sheet: 0.95 (0.39), residues: 168 loop : -0.72 (0.21), residues: 936 =============================================================================== Job complete usr+sys time: 14011.92 seconds wall clock time: 244 minutes 44.83 seconds (14684.83 seconds total)