Starting phenix.real_space_refine on Sun Feb 25 04:08:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/02_2024/7u67_26362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/02_2024/7u67_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_26362/02_2024/7u67_26362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/02_2024/7u67_26362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/02_2024/7u67_26362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u67_26362/02_2024/7u67_26362_updated.pdb" } resolution = 2.5 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= 0.006 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 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. 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 14.03, per 1000 atoms: 0.52 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: 11.15 Conformation dependent library (CDL) restraints added in 5.4 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: 5.17 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: 7.47 Time building geometry restraints manager: 11.87 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 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.340 Construct map_model_manager: 0.040 Extract box with map and model: 4.360 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 69.620 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.170 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.91 % Allowed : 16.67 % Favored : 82.42 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 73 HIS 0.003 0.001 HIS E 445 PHE 0.013 0.001 PHE E 286 TYR 0.018 0.001 TYR B 272 ARG 0.006 0.000 ARG D 154 *********************** 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 : 3.176 Fit side-chains REVERT: A 192 LEU cc_start: 0.8518 (tp) cc_final: 0.8295 (tp) REVERT: A 286 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7396 (p90) REVERT: A 382 TYR cc_start: 0.8069 (m-80) cc_final: 0.7609 (m-80) REVERT: A 398 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.7129 (ttp-110) REVERT: A 400 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 499 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7163 (mtp180) REVERT: D 26 HIS cc_start: 0.7694 (t70) cc_final: 0.7489 (t70) REVERT: D 82 LYS cc_start: 0.7860 (mttp) cc_final: 0.7658 (mttm) REVERT: D 174 ARG cc_start: 0.8160 (ptp90) cc_final: 0.7949 (ptm160) REVERT: D 237 LEU cc_start: 0.8453 (tp) cc_final: 0.8163 (tt) REVERT: D 382 TYR cc_start: 0.8161 (m-80) cc_final: 0.7865 (m-80) REVERT: D 398 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.6661 (ttp-110) REVERT: D 498 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7497 (mtm-85) REVERT: C 66 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7451 (mtt-85) REVERT: C 82 LYS cc_start: 0.7959 (mttp) cc_final: 0.7731 (mttm) REVERT: C 118 ASP cc_start: 0.6854 (m-30) cc_final: 0.6555 (t0) REVERT: C 134 ASP cc_start: 0.7775 (m-30) cc_final: 0.7562 (m-30) REVERT: C 237 LEU cc_start: 0.8487 (tp) cc_final: 0.8239 (tt) REVERT: C 382 TYR cc_start: 0.8154 (m-80) cc_final: 0.7840 (m-80) REVERT: C 398 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.6737 (ttp-110) REVERT: C 421 SER cc_start: 0.8214 (m) cc_final: 0.8005 (p) REVERT: B 23 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8389 (mmmt) REVERT: B 66 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7397 (mtt-85) REVERT: B 154 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8094 (mtm-85) REVERT: B 184 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6441 (tm-30) REVERT: B 382 TYR cc_start: 0.7975 (m-80) cc_final: 0.7501 (m-80) REVERT: B 434 VAL cc_start: 0.8148 (t) cc_final: 0.7860 (t) REVERT: F 75 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7930 (tp40) REVERT: F 382 TYR cc_start: 0.7812 (m-80) cc_final: 0.7587 (m-80) REVERT: F 499 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7192 (mtp180) REVERT: E 66 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7378 (mtt-85) REVERT: E 134 ASP cc_start: 0.7761 (m-30) cc_final: 0.7511 (m-30) REVERT: E 154 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7991 (mtm180) REVERT: E 217 TRP cc_start: 0.8819 (p-90) cc_final: 0.8308 (p90) REVERT: E 382 TYR cc_start: 0.8017 (m-80) cc_final: 0.7711 (m-80) REVERT: E 473 GLU cc_start: 0.6680 (tm-30) cc_final: 0.6469 (tm-30) REVERT: E 498 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7867 (mtp180) REVERT: E 499 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7195 (mtp180) outliers start: 24 outliers final: 9 residues processed: 575 average time/residue: 1.8492 time to fit residues: 1185.3701 Evaluate side-chains 534 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 521 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain K residue 40 CYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 499 ARG Chi-restraints excluded: chain E residue 499 ARG 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: 1.9990 chunk 133 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 299 optimal weight: 0.8980 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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: 0.7555 moved from start: 0.1267 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= 0.159 Angle : 0.501 7.935 37356 Z= 0.254 Chirality : 0.038 0.117 4140 Planarity : 0.004 0.038 4668 Dihedral : 11.957 171.428 3818 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.09 % Allowed : 17.47 % Favored : 80.44 % 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: 0.67 (0.15), residues: 3264 helix: 0.89 (0.11), residues: 2160 sheet: 1.65 (0.43), residues: 162 loop : -0.65 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 73 HIS 0.010 0.001 HIS D 445 PHE 0.009 0.001 PHE C 106 TYR 0.011 0.001 TYR J 28 ARG 0.009 0.000 ARG F 64 *********************** 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 584 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 529 time to evaluate : 3.024 Fit side-chains REVERT: A 75 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7740 (tp40) REVERT: A 192 LEU cc_start: 0.8519 (tp) cc_final: 0.8301 (tp) REVERT: A 286 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7298 (p90) REVERT: A 382 TYR cc_start: 0.7808 (m-80) cc_final: 0.7516 (m-80) REVERT: A 397 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7510 (mt-10) REVERT: A 499 ARG cc_start: 0.7612 (mtp180) cc_final: 0.7290 (mtp180) REVERT: K 73 TRP cc_start: 0.7383 (t60) cc_final: 0.7075 (t60) REVERT: D 41 ASN cc_start: 0.8366 (m110) cc_final: 0.8140 (m110) REVERT: D 237 LEU cc_start: 0.8185 (tp) cc_final: 0.7937 (tt) REVERT: D 291 LEU cc_start: 0.7672 (tp) cc_final: 0.7399 (tp) REVERT: D 382 TYR cc_start: 0.7842 (m-80) cc_final: 0.7533 (m-80) REVERT: D 498 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7575 (mtp180) REVERT: C 237 LEU cc_start: 0.8216 (tp) cc_final: 0.8011 (tt) REVERT: C 291 LEU cc_start: 0.7652 (tp) cc_final: 0.7379 (tp) REVERT: C 382 TYR cc_start: 0.7823 (m-80) cc_final: 0.7560 (m-80) REVERT: C 469 PHE cc_start: 0.8333 (t80) cc_final: 0.8042 (t80) REVERT: B 33 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7309 (mp0) REVERT: B 66 ARG cc_start: 0.7465 (mtp85) cc_final: 0.7154 (mtt-85) REVERT: B 154 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8097 (mtm-85) REVERT: B 184 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6395 (tm-30) REVERT: B 434 VAL cc_start: 0.8140 (t) cc_final: 0.7852 (t) REVERT: B 491 LEU cc_start: 0.8276 (mp) cc_final: 0.7855 (mm) REVERT: B 495 ASP cc_start: 0.7114 (m-30) cc_final: 0.6900 (m-30) REVERT: F 75 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7725 (tp40) REVERT: F 286 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7282 (p90) REVERT: F 347 TYR cc_start: 0.8170 (t80) cc_final: 0.7941 (t80) REVERT: F 382 TYR cc_start: 0.7556 (m-80) cc_final: 0.7249 (m-80) REVERT: F 397 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7592 (mt-10) REVERT: F 421 SER cc_start: 0.8063 (m) cc_final: 0.7844 (t) REVERT: E 33 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7171 (mp0) REVERT: E 134 ASP cc_start: 0.7811 (m-30) cc_final: 0.7506 (m-30) REVERT: E 154 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.8035 (mtm180) REVERT: E 217 TRP cc_start: 0.8792 (p-90) cc_final: 0.8332 (p90) REVERT: E 473 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6413 (tm-30) REVERT: E 499 ARG cc_start: 0.7393 (mtp180) cc_final: 0.7105 (mtp180) outliers start: 55 outliers final: 11 residues processed: 555 average time/residue: 1.7696 time to fit residues: 1101.2477 Evaluate side-chains 532 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 517 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain I residue 75 ASN Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain E residue 422 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 300 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 297 optimal weight: 0.0070 chunk 102 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.1650 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= 0.158 Angle : 0.478 7.264 37356 Z= 0.238 Chirality : 0.037 0.122 4140 Planarity : 0.004 0.038 4668 Dihedral : 11.333 175.462 3800 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.55 % Allowed : 17.43 % Favored : 80.02 % 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: 1.16 (0.11), residues: 2166 sheet: 1.74 (0.41), residues: 162 loop : -0.63 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 73 HIS 0.010 0.001 HIS D 445 PHE 0.012 0.001 PHE D 106 TYR 0.021 0.001 TYR E 382 ARG 0.006 0.000 ARG A 64 *********************** 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 590 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 523 time to evaluate : 3.315 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7772 (tp40) REVERT: A 286 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7323 (p90) REVERT: A 382 TYR cc_start: 0.7789 (m-80) cc_final: 0.7481 (m-80) REVERT: A 499 ARG cc_start: 0.7624 (mtp180) cc_final: 0.7271 (mtp180) REVERT: D 41 ASN cc_start: 0.8433 (m110) cc_final: 0.8214 (m110) REVERT: D 75 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: D 137 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7785 (ttp80) REVERT: D 237 LEU cc_start: 0.8179 (tp) cc_final: 0.7969 (tt) REVERT: D 382 TYR cc_start: 0.7828 (m-80) cc_final: 0.7534 (m-80) REVERT: D 498 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7559 (mtp180) REVERT: C 75 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: C 184 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6155 (tm-30) REVERT: C 382 TYR cc_start: 0.7774 (m-80) cc_final: 0.7554 (m-80) REVERT: C 469 PHE cc_start: 0.8321 (t80) cc_final: 0.8026 (t80) REVERT: B 64 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7242 (mtm-85) REVERT: B 66 ARG cc_start: 0.7436 (mtp85) cc_final: 0.7144 (mtt-85) REVERT: B 184 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6530 (tm-30) REVERT: B 382 TYR cc_start: 0.7845 (m-10) cc_final: 0.7595 (m-80) REVERT: B 421 SER cc_start: 0.8003 (m) cc_final: 0.7791 (p) REVERT: B 440 GLU cc_start: 0.6953 (mp0) cc_final: 0.6637 (mp0) REVERT: F 75 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7727 (tp40) REVERT: F 286 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7300 (p90) REVERT: F 382 TYR cc_start: 0.7563 (m-80) cc_final: 0.7282 (m-80) REVERT: F 397 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7567 (mt-10) REVERT: E 154 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.8043 (mtm180) REVERT: E 184 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6526 (tm-30) REVERT: E 217 TRP cc_start: 0.8790 (p-90) cc_final: 0.8358 (p90) REVERT: E 440 GLU cc_start: 0.6890 (mp0) cc_final: 0.6621 (mp0) REVERT: E 473 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6431 (tm-30) outliers start: 67 outliers final: 17 residues processed: 550 average time/residue: 1.8442 time to fit residues: 1134.1899 Evaluate side-chains 545 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 520 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 434 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 8.9990 chunk 225 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 201 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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: 0.7606 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27456 Z= 0.303 Angle : 0.555 8.255 37356 Z= 0.279 Chirality : 0.041 0.149 4140 Planarity : 0.004 0.040 4668 Dihedral : 11.233 178.415 3800 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.12 % Allowed : 17.24 % Favored : 79.64 % 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: 0.76 (0.15), residues: 3264 helix: 1.08 (0.11), residues: 2148 sheet: 1.52 (0.38), residues: 162 loop : -0.89 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 73 HIS 0.009 0.001 HIS D 445 PHE 0.023 0.002 PHE E 286 TYR 0.017 0.002 TYR E 382 ARG 0.005 0.001 ARG F 154 *********************** 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 607 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 525 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: A 286 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7347 (p90) REVERT: A 382 TYR cc_start: 0.7812 (m-80) cc_final: 0.7511 (m-80) REVERT: A 400 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6787 (mt-10) REVERT: D 75 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: D 137 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7755 (ttp80) REVERT: D 184 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6671 (tm-30) REVERT: D 469 PHE cc_start: 0.8439 (t80) cc_final: 0.8208 (t80) REVERT: D 498 ARG cc_start: 0.7967 (mtp-110) cc_final: 0.7486 (mtm-85) REVERT: C 75 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: C 82 LYS cc_start: 0.7915 (mttp) cc_final: 0.7562 (mttm) REVERT: C 469 PHE cc_start: 0.8343 (t80) cc_final: 0.8074 (t80) REVERT: B 64 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7289 (mtm-85) REVERT: B 66 ARG cc_start: 0.7580 (mtp85) cc_final: 0.7217 (mtt-85) REVERT: B 75 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: B 184 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6711 (tm-30) REVERT: B 440 GLU cc_start: 0.7006 (mp0) cc_final: 0.6690 (mp0) REVERT: F 75 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: F 197 MET cc_start: 0.7816 (mmt) cc_final: 0.7433 (mmt) REVERT: F 286 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7291 (p90) REVERT: F 382 TYR cc_start: 0.7625 (m-80) cc_final: 0.7339 (m-80) REVERT: F 400 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6875 (mt-10) REVERT: E 154 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8005 (mtm-85) REVERT: E 217 TRP cc_start: 0.8783 (p-90) cc_final: 0.8352 (p90) REVERT: E 382 TYR cc_start: 0.7936 (m-10) cc_final: 0.7668 (m-80) REVERT: E 440 GLU cc_start: 0.6921 (mp0) cc_final: 0.6653 (mp0) REVERT: E 473 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6458 (tm-30) outliers start: 82 outliers final: 31 residues processed: 567 average time/residue: 1.7942 time to fit residues: 1139.4265 Evaluate side-chains 563 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 523 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 459 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 237 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 220 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 251 ASN F 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27456 Z= 0.261 Angle : 0.523 8.720 37356 Z= 0.263 Chirality : 0.040 0.169 4140 Planarity : 0.004 0.040 4668 Dihedral : 11.031 177.268 3800 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.23 % Allowed : 18.26 % Favored : 78.50 % 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: 0.78 (0.15), residues: 3264 helix: 1.08 (0.12), residues: 2160 sheet: 1.43 (0.39), residues: 162 loop : -0.85 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 73 HIS 0.010 0.001 HIS D 445 PHE 0.020 0.002 PHE E 286 TYR 0.013 0.002 TYR B 382 ARG 0.006 0.000 ARG F 154 *********************** 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 606 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 521 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: A 286 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7339 (p90) REVERT: A 382 TYR cc_start: 0.7797 (m-80) cc_final: 0.7486 (m-80) REVERT: D 75 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: D 137 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7448 (ttp80) REVERT: D 184 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6699 (tm-30) REVERT: D 498 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7476 (mtm-85) REVERT: C 75 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: C 82 LYS cc_start: 0.7920 (mttp) cc_final: 0.7567 (mttm) REVERT: C 121 ASN cc_start: 0.8383 (m-40) cc_final: 0.8163 (m-40) REVERT: C 184 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6369 (tm-30) REVERT: B 64 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7270 (mtm-85) REVERT: B 66 ARG cc_start: 0.7530 (mtp85) cc_final: 0.7228 (mtt-85) REVERT: B 75 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: B 184 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6722 (tm-30) REVERT: B 440 GLU cc_start: 0.7006 (mp0) cc_final: 0.6693 (mp0) REVERT: F 75 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: F 286 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7306 (p90) REVERT: F 382 TYR cc_start: 0.7629 (m-80) cc_final: 0.7359 (m-80) REVERT: F 400 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6814 (mt-10) REVERT: E 75 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: E 154 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.8052 (mtm-85) REVERT: E 217 TRP cc_start: 0.8771 (p-90) cc_final: 0.8363 (p90) REVERT: E 317 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: E 440 GLU cc_start: 0.6933 (mp0) cc_final: 0.6697 (mp0) REVERT: E 473 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6413 (tm-30) outliers start: 85 outliers final: 47 residues processed: 568 average time/residue: 1.7820 time to fit residues: 1134.8306 Evaluate side-chains 580 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 522 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain E residue 459 VAL 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: 0.0170 chunk 63 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 319 optimal weight: 0.5980 chunk 265 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN D 290 GLN D 445 HIS E 445 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27456 Z= 0.135 Angle : 0.460 12.518 37356 Z= 0.229 Chirality : 0.037 0.123 4140 Planarity : 0.004 0.040 4668 Dihedral : 10.754 174.747 3800 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.93 % Allowed : 19.06 % Favored : 78.01 % 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: 1.08 (0.15), residues: 3264 helix: 1.27 (0.12), residues: 2172 sheet: 1.46 (0.39), residues: 162 loop : -0.61 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP G 73 HIS 0.012 0.001 HIS D 445 PHE 0.009 0.001 PHE E 286 TYR 0.014 0.001 TYR E 382 ARG 0.007 0.000 ARG A 64 *********************** 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 599 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 522 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7592 (tmt170) REVERT: A 75 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7773 (tp40) REVERT: A 286 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7300 (p90) REVERT: A 382 TYR cc_start: 0.7740 (m-80) cc_final: 0.7473 (m-80) REVERT: D 75 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: D 137 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7439 (ttp80) REVERT: D 184 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6689 (tm-30) REVERT: D 498 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7491 (mtm-85) REVERT: C 75 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: C 82 LYS cc_start: 0.7937 (mttp) cc_final: 0.7689 (mttm) REVERT: C 121 ASN cc_start: 0.8374 (m-40) cc_final: 0.8165 (m-40) REVERT: C 184 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6248 (tm-30) REVERT: C 382 TYR cc_start: 0.7714 (m-80) cc_final: 0.7498 (m-80) REVERT: B 66 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7098 (mtt-85) REVERT: B 184 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6669 (tm-30) REVERT: B 186 ASN cc_start: 0.8632 (m-40) cc_final: 0.8346 (m110) REVERT: B 412 GLU cc_start: 0.7250 (tp30) cc_final: 0.7047 (tp30) REVERT: B 440 GLU cc_start: 0.6963 (mp0) cc_final: 0.6657 (mp0) REVERT: F 75 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7722 (tp40) REVERT: F 82 LYS cc_start: 0.7949 (mttp) cc_final: 0.7716 (mttp) REVERT: F 286 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7295 (p90) REVERT: F 317 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: F 382 TYR cc_start: 0.7573 (m-80) cc_final: 0.7350 (m-80) REVERT: E 78 ARG cc_start: 0.8016 (ttt180) cc_final: 0.7754 (ttt90) REVERT: E 154 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8067 (mtm-85) REVERT: E 184 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6636 (tm-30) REVERT: E 217 TRP cc_start: 0.8744 (p-90) cc_final: 0.8383 (p90) REVERT: E 317 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: E 440 GLU cc_start: 0.6904 (mp0) cc_final: 0.6661 (mp0) REVERT: E 473 GLU cc_start: 0.6613 (tm-30) cc_final: 0.6405 (mm-30) REVERT: E 499 ARG cc_start: 0.7357 (mtp180) cc_final: 0.7121 (mtp180) outliers start: 77 outliers final: 32 residues processed: 565 average time/residue: 1.8516 time to fit residues: 1172.3674 Evaluate side-chains 566 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 524 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 422 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 chunk 178 optimal weight: 0.0470 chunk 318 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 193 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN D 445 HIS B 342 ASN E 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 27456 Z= 0.127 Angle : 0.452 6.561 37356 Z= 0.225 Chirality : 0.037 0.147 4140 Planarity : 0.004 0.038 4668 Dihedral : 10.597 174.973 3800 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.98 % Allowed : 20.24 % Favored : 77.78 % 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: 1.22 (0.15), residues: 3264 helix: 1.36 (0.12), residues: 2172 sheet: 1.54 (0.39), residues: 162 loop : -0.53 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 73 HIS 0.013 0.001 HIS D 445 PHE 0.010 0.001 PHE C 444 TYR 0.014 0.001 TYR B 382 ARG 0.007 0.000 ARG F 499 *********************** 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 580 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 528 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7581 (tmt170) REVERT: A 75 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7776 (tp40) REVERT: A 286 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.7263 (p90) REVERT: A 382 TYR cc_start: 0.7726 (m-80) cc_final: 0.7468 (m-80) REVERT: D 75 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: D 137 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7470 (ttp80) REVERT: D 184 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6713 (tm-30) REVERT: D 498 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7493 (mtm-85) REVERT: C 82 LYS cc_start: 0.7966 (mttp) cc_final: 0.7737 (mttm) REVERT: C 121 ASN cc_start: 0.8378 (m-40) cc_final: 0.8169 (m-40) REVERT: C 184 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6187 (tm-30) REVERT: C 382 TYR cc_start: 0.7696 (m-80) cc_final: 0.7489 (m-80) REVERT: B 66 ARG cc_start: 0.7392 (mtp85) cc_final: 0.7102 (mtt-85) REVERT: B 184 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6666 (tm-30) REVERT: B 186 ASN cc_start: 0.8632 (m-40) cc_final: 0.8337 (m110) REVERT: B 440 GLU cc_start: 0.6958 (mp0) cc_final: 0.6649 (mp0) REVERT: F 75 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: F 82 LYS cc_start: 0.7945 (mttp) cc_final: 0.7715 (mttp) REVERT: F 239 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6458 (mm-30) REVERT: F 286 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7260 (p90) REVERT: F 382 TYR cc_start: 0.7555 (m-80) cc_final: 0.7331 (m-80) REVERT: E 154 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.8072 (mtm-85) REVERT: E 184 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6630 (tm-30) REVERT: E 217 TRP cc_start: 0.8748 (p-90) cc_final: 0.8384 (p90) REVERT: E 317 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: E 382 TYR cc_start: 0.7823 (m-10) cc_final: 0.7511 (m-80) REVERT: E 440 GLU cc_start: 0.6877 (mp0) cc_final: 0.6641 (mp0) REVERT: E 499 ARG cc_start: 0.7354 (mtp180) cc_final: 0.7120 (mtp180) outliers start: 52 outliers final: 32 residues processed: 550 average time/residue: 1.8491 time to fit residues: 1139.5376 Evaluate side-chains 560 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 519 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 317 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 157 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 250 optimal weight: 0.0980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN D 445 HIS C 41 ASN B 178 GLN B 342 ASN E 227 HIS E 294 HIS E 365 ASN E 389 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2248 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= 0.427 Angle : 0.606 7.890 37356 Z= 0.307 Chirality : 0.045 0.157 4140 Planarity : 0.005 0.042 4668 Dihedral : 10.896 178.937 3800 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.89 % Allowed : 19.82 % Favored : 77.28 % 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: 0.69 (0.15), residues: 3264 helix: 1.01 (0.11), residues: 2160 sheet: 1.43 (0.40), residues: 162 loop : -0.89 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 73 HIS 0.013 0.002 HIS D 445 PHE 0.029 0.003 PHE E 286 TYR 0.018 0.002 TYR J 28 ARG 0.010 0.001 ARG F 499 *********************** 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 605 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 529 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7441 (tmt170) REVERT: A 75 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: A 286 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7343 (p90) REVERT: A 382 TYR cc_start: 0.7814 (m-80) cc_final: 0.7495 (m-80) REVERT: D 75 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: D 137 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7465 (ttp80) REVERT: C 66 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7517 (mtt-85) REVERT: C 75 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: C 382 TYR cc_start: 0.7803 (m-80) cc_final: 0.7577 (m-80) REVERT: B 64 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7299 (mtm-85) REVERT: B 66 ARG cc_start: 0.7618 (mtp85) cc_final: 0.7199 (mtt-85) REVERT: B 184 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6763 (tm-30) REVERT: B 186 ASN cc_start: 0.8647 (m-40) cc_final: 0.8342 (m110) REVERT: B 440 GLU cc_start: 0.7021 (mp0) cc_final: 0.6716 (mp0) REVERT: B 453 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8322 (mp) REVERT: F 75 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: F 286 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7357 (p90) REVERT: F 382 TYR cc_start: 0.7645 (m-80) cc_final: 0.7347 (m-80) REVERT: F 400 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6948 (mt-10) REVERT: E 75 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: E 154 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.8066 (mtm-85) REVERT: E 217 TRP cc_start: 0.8761 (p-90) cc_final: 0.8373 (p90) REVERT: E 317 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: E 382 TYR cc_start: 0.7871 (m-10) cc_final: 0.7549 (m-80) REVERT: E 440 GLU cc_start: 0.6940 (mp0) cc_final: 0.6695 (mp0) REVERT: E 499 ARG cc_start: 0.7386 (mtp180) cc_final: 0.7125 (mtp180) outliers start: 76 outliers final: 48 residues processed: 572 average time/residue: 1.8002 time to fit residues: 1153.4023 Evaluate side-chains 585 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 525 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain E residue 459 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.8980 chunk 304 optimal weight: 0.0270 chunk 278 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 267 optimal weight: 0.4980 chunk 280 optimal weight: 0.5980 chunk 295 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN D 11 ASN D 445 HIS B 342 ASN F 74 GLN E 342 ASN E 365 ASN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2298 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= 0.133 Angle : 0.468 7.982 37356 Z= 0.235 Chirality : 0.037 0.137 4140 Planarity : 0.004 0.040 4668 Dihedral : 10.632 176.499 3800 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.13 % Allowed : 21.08 % Favored : 76.79 % 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: 1.03 (0.15), residues: 3264 helix: 1.25 (0.12), residues: 2166 sheet: 1.44 (0.40), residues: 162 loop : -0.69 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 73 HIS 0.015 0.001 HIS D 445 PHE 0.011 0.001 PHE A 106 TYR 0.011 0.001 TYR B 382 ARG 0.008 0.000 ARG F 499 *********************** 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 581 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 525 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7604 (tmt170) REVERT: A 286 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7282 (p90) REVERT: A 382 TYR cc_start: 0.7730 (m-80) cc_final: 0.7465 (m-80) REVERT: D 75 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: D 137 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7432 (ttp80) REVERT: C 75 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: C 121 ASN cc_start: 0.8390 (m-40) cc_final: 0.8182 (m-40) REVERT: C 184 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6272 (tm-30) REVERT: C 382 TYR cc_start: 0.7724 (m-80) cc_final: 0.7491 (m-80) REVERT: B 66 ARG cc_start: 0.7420 (mtp85) cc_final: 0.7007 (mtt-85) REVERT: B 75 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: B 184 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6686 (tm-30) REVERT: B 186 ASN cc_start: 0.8631 (m-40) cc_final: 0.8360 (m110) REVERT: B 412 GLU cc_start: 0.7218 (tp30) cc_final: 0.6989 (tp30) REVERT: F 75 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: F 82 LYS cc_start: 0.7932 (mttp) cc_final: 0.7607 (mttp) REVERT: F 286 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7249 (p90) REVERT: F 382 TYR cc_start: 0.7575 (m-80) cc_final: 0.7335 (m-80) REVERT: E 154 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.8070 (mtm-85) REVERT: E 184 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6632 (tm-30) REVERT: E 217 TRP cc_start: 0.8733 (p-90) cc_final: 0.8391 (p90) REVERT: E 239 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6590 (mm-30) REVERT: E 317 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: E 440 GLU cc_start: 0.6895 (mp0) cc_final: 0.6659 (mp0) REVERT: E 499 ARG cc_start: 0.7335 (mtp180) cc_final: 0.7093 (mtp180) outliers start: 56 outliers final: 32 residues processed: 549 average time/residue: 1.8617 time to fit residues: 1142.4812 Evaluate side-chains 562 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 520 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 426 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 1.9990 chunk 313 optimal weight: 6.9990 chunk 191 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 302 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN D 445 HIS B 178 GLN B 294 HIS B 342 ASN E 365 ASN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27456 Z= 0.180 Angle : 0.496 11.195 37356 Z= 0.247 Chirality : 0.038 0.133 4140 Planarity : 0.004 0.041 4668 Dihedral : 10.592 176.066 3800 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.79 % Allowed : 21.54 % Favored : 76.67 % 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: 1.06 (0.15), residues: 3264 helix: 1.25 (0.12), residues: 2172 sheet: 1.42 (0.40), residues: 162 loop : -0.63 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP J 73 HIS 0.017 0.001 HIS D 445 PHE 0.014 0.001 PHE E 286 TYR 0.015 0.001 TYR B 382 ARG 0.010 0.000 ARG F 499 ********************** 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 570 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 523 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7492 (tmt170) REVERT: A 286 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7280 (p90) REVERT: A 382 TYR cc_start: 0.7753 (m-80) cc_final: 0.7484 (m-80) REVERT: D 75 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: D 137 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7454 (ttp80) REVERT: D 382 TYR cc_start: 0.7873 (m-10) cc_final: 0.7567 (m-80) REVERT: C 75 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: C 121 ASN cc_start: 0.8395 (m-40) cc_final: 0.8188 (m-40) REVERT: C 184 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6267 (tm-30) REVERT: C 382 TYR cc_start: 0.7721 (m-80) cc_final: 0.7506 (m-80) REVERT: B 66 ARG cc_start: 0.7475 (mtp85) cc_final: 0.7075 (mtt-85) REVERT: B 184 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6703 (tm-30) REVERT: B 186 ASN cc_start: 0.8639 (m-40) cc_final: 0.8342 (m110) REVERT: F 75 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: F 197 MET cc_start: 0.7797 (mmt) cc_final: 0.7413 (mmt) REVERT: F 286 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7253 (p90) REVERT: F 382 TYR cc_start: 0.7584 (m-80) cc_final: 0.7347 (m-80) REVERT: E 154 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.8047 (mtm-85) REVERT: E 184 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6638 (tm-30) REVERT: E 217 TRP cc_start: 0.8746 (p-90) cc_final: 0.8375 (p90) REVERT: E 317 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: E 440 GLU cc_start: 0.6894 (mp0) cc_final: 0.6645 (mp0) REVERT: E 499 ARG cc_start: 0.7360 (mtp180) cc_final: 0.7125 (mtp180) outliers start: 47 outliers final: 29 residues processed: 545 average time/residue: 1.8329 time to fit residues: 1117.5672 Evaluate side-chains 557 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 520 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 317 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 426 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.0770 chunk 278 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN D 445 HIS B 342 ASN E 365 ASN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118485 restraints weight = 33805.056| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.37 r_work: 0.3453 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27456 Z= 0.142 Angle : 0.476 10.834 37356 Z= 0.238 Chirality : 0.037 0.197 4140 Planarity : 0.004 0.039 4668 Dihedral : 10.480 176.656 3800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.45 % Allowed : 21.96 % Favored : 76.60 % 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: 1.16 (0.15), residues: 3264 helix: 1.33 (0.12), residues: 2166 sheet: 1.47 (0.40), residues: 162 loop : -0.58 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP J 73 HIS 0.017 0.001 HIS D 445 PHE 0.009 0.001 PHE D 286 TYR 0.015 0.001 TYR B 382 ARG 0.010 0.000 ARG F 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14860.92 seconds wall clock time: 263 minutes 18.07 seconds (15798.07 seconds total)