Starting phenix.real_space_refine on Sat Feb 17 05:36:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf8_12298/02_2024/7nf8_12298_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf8_12298/02_2024/7nf8_12298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf8_12298/02_2024/7nf8_12298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf8_12298/02_2024/7nf8_12298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf8_12298/02_2024/7nf8_12298_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf8_12298/02_2024/7nf8_12298_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 2 5.49 5 S 98 5.16 5 C 11508 2.51 5 N 2834 2.21 5 O 3190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 664": "OD1" <-> "OD2" Residue "A ARG 665": "NH1" <-> "NH2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E ARG 205": "NH1" <-> "NH2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E GLU 282": "OE1" <-> "OE2" Residue "E TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 405": "NH1" <-> "NH2" Residue "E GLU 478": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F ASP 241": "OD1" <-> "OD2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F GLU 268": "OE1" <-> "OE2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ASP 349": "OD1" <-> "OD2" Residue "F ARG 362": "NH1" <-> "NH2" Residue "F ARG 365": "NH1" <-> "NH2" Residue "F ARG 377": "NH1" <-> "NH2" Residue "F GLU 388": "OE1" <-> "OE2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F ARG 452": "NH1" <-> "NH2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F GLU 562": "OE1" <-> "OE2" Residue "F TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 574": "NH1" <-> "NH2" Residue "F ARG 584": "NH1" <-> "NH2" Residue "F GLU 585": "OE1" <-> "OE2" Residue "F PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 601": "OE1" <-> "OE2" Residue "F ARG 617": "NH1" <-> "NH2" Residue "F ARG 619": "NH1" <-> "NH2" Residue "F ARG 631": "NH1" <-> "NH2" Residue "F GLU 632": "OE1" <-> "OE2" Residue "F GLU 649": "OE1" <-> "OE2" Residue "F TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 664": "OD1" <-> "OD2" Residue "F ARG 665": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17634 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3506 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 25, 'TRANS': 429} Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5090 Classifications: {'peptide': 623} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 596} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 109 Unusual residues: {' CA': 1, 'LBN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3506 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 25, 'TRANS': 429} Chain: "F" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5090 Classifications: {'peptide': 623} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 596} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 109 Unusual residues: {' CA': 1, 'LBN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.64, per 1000 atoms: 0.55 Number of scatterers: 17634 At special positions: 0 Unit cell: (135.123, 119.743, 139.517, 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) Ca 2 19.99 S 98 16.00 P 2 15.00 O 3190 8.00 N 2834 7.00 C 11508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS A 114 " distance=2.08 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.04 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS F 114 " distance=2.08 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS F 273 " distance=2.03 Simple disulfide: pdb=" SG CYS F 571 " - pdb=" SG CYS F 666 " distance=2.04 Simple disulfide: pdb=" SG CYS F 673 " - pdb=" SG CYS F 685 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 703 " - " ASN A 513 " " NAG A 704 " - " ASN A 246 " " NAG A 705 " - " ASN A 228 " " NAG A 706 " - " ASN A 523 " " NAG C 1 " - " ASN A 332 " " NAG D 1 " - " ASN A 261 " " NAG F 703 " - " ASN F 513 " " NAG F 704 " - " ASN F 246 " " NAG F 705 " - " ASN F 228 " " NAG F 706 " - " ASN F 523 " " NAG G 1 " - " ASN F 332 " " NAG H 1 " - " ASN F 261 " Time building additional restraints: 6.96 Conformation dependent library (CDL) restraints added in 3.5 seconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 10 sheets defined 48.1% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'B' and resid 32 through 43 removed outlier: 4.439A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.950A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 89 removed outlier: 4.078A pdb=" N TRP B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 86 " --> pdb=" O CYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.702A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 3.635A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 136 removed outlier: 3.709A pdb=" N SER B 133 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 148 through 168 removed outlier: 3.771A pdb=" N ALA B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 177 through 200 removed outlier: 3.529A pdb=" N ALA B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.585A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.550A pdb=" N GLU B 243 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.587A pdb=" N MET B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 4.199A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 285' Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.647A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 333 removed outlier: 3.501A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 324 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY B 325 " --> pdb=" O CYS B 321 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 352 through 368 removed outlier: 3.502A pdb=" N MET B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 371 through 398 removed outlier: 3.605A pdb=" N ASN B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 390 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 removed outlier: 3.774A pdb=" N ILE B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 435 through 454 removed outlier: 3.563A pdb=" N TYR B 439 " --> pdb=" O TRP B 435 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 444 " --> pdb=" O CYS B 440 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 removed outlier: 3.943A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 464' Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.829A pdb=" N MET B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.544A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 76' Processing helix chain 'A' and resid 84 through 110 removed outlier: 3.645A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.698A pdb=" N THR A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.599A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.761A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 355 through 369 removed outlier: 4.404A pdb=" N HIS A 358 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 359 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 361 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 362 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.664A pdb=" N VAL A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 459 through 471 removed outlier: 4.892A pdb=" N ASN A 463 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 464 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 465 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 467 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 468 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 469 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 470 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 518 Processing helix chain 'A' and resid 538 through 541 No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.529A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 607 through 610 No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'E' and resid 32 through 43 removed outlier: 4.439A pdb=" N ILE E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 41 " --> pdb=" O CYS E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.950A pdb=" N ASN E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 89 removed outlier: 4.078A pdb=" N TRP E 69 " --> pdb=" O CYS E 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 86 " --> pdb=" O CYS E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 103 removed outlier: 3.702A pdb=" N ALA E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 118 removed outlier: 3.635A pdb=" N LEU E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 136 removed outlier: 3.709A pdb=" N SER E 133 " --> pdb=" O CYS E 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 148 through 168 removed outlier: 3.771A pdb=" N ALA E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 177 through 200 removed outlier: 3.529A pdb=" N ALA E 182 " --> pdb=" O ASN E 178 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 232 removed outlier: 3.585A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 231 " --> pdb=" O ASN E 227 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR E 232 " --> pdb=" O GLY E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.550A pdb=" N GLU E 243 " --> pdb=" O TYR E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 257 Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.587A pdb=" N MET E 270 " --> pdb=" O CYS E 266 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE E 275 " --> pdb=" O ASN E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 removed outlier: 4.199A pdb=" N LEU E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 285' Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.647A pdb=" N ARG E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 333 removed outlier: 3.501A pdb=" N ALA E 310 " --> pdb=" O PRO E 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY E 325 " --> pdb=" O CYS E 321 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 342 Processing helix chain 'E' and resid 352 through 368 removed outlier: 3.502A pdb=" N MET E 360 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 361 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA E 362 " --> pdb=" O HIS E 358 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 364 " --> pdb=" O MET E 360 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) Proline residue: E 368 - end of helix Processing helix chain 'E' and resid 371 through 398 removed outlier: 3.605A pdb=" N ASN E 376 " --> pdb=" O ASN E 372 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 390 " --> pdb=" O TYR E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 431 removed outlier: 3.774A pdb=" N ILE E 415 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE E 423 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Proline residue: E 428 - end of helix Processing helix chain 'E' and resid 435 through 454 removed outlier: 3.563A pdb=" N TYR E 439 " --> pdb=" O TRP E 435 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET E 444 " --> pdb=" O CYS E 440 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE E 452 " --> pdb=" O LEU E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 464 removed outlier: 3.943A pdb=" N LYS E 464 " --> pdb=" O GLY E 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 460 through 464' Processing helix chain 'E' and resid 467 through 477 removed outlier: 3.829A pdb=" N MET E 471 " --> pdb=" O LYS E 467 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS E 472 " --> pdb=" O PRO E 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 76 removed outlier: 3.544A pdb=" N PHE F 74 " --> pdb=" O LYS F 70 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 70 through 76' Processing helix chain 'F' and resid 84 through 110 removed outlier: 3.645A pdb=" N ALA F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE F 105 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 120 No H-bonds generated for 'chain 'F' and resid 117 through 120' Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 149 through 154 removed outlier: 3.698A pdb=" N THR F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 190 through 203 removed outlier: 3.599A pdb=" N LYS F 203 " --> pdb=" O ALA F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 227 Processing helix chain 'F' and resid 231 through 235 removed outlier: 3.761A pdb=" N THR F 234 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP F 235 " --> pdb=" O LYS F 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 231 through 235' Processing helix chain 'F' and resid 290 through 305 Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 355 through 369 removed outlier: 4.404A pdb=" N HIS F 358 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 359 " --> pdb=" O GLY F 356 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL F 361 " --> pdb=" O HIS F 358 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG F 362 " --> pdb=" O ASP F 359 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 365 " --> pdb=" O ARG F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 397 Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 421 through 434 removed outlier: 3.664A pdb=" N VAL F 427 " --> pdb=" O SER F 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN F 434 " --> pdb=" O SER F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 456 No H-bonds generated for 'chain 'F' and resid 453 through 456' Processing helix chain 'F' and resid 459 through 471 removed outlier: 4.892A pdb=" N ASN F 463 " --> pdb=" O LYS F 460 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE F 464 " --> pdb=" O TYR F 461 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET F 465 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET F 467 " --> pdb=" O ILE F 464 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 468 " --> pdb=" O MET F 465 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL F 469 " --> pdb=" O ASN F 466 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 470 " --> pdb=" O MET F 467 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 471 " --> pdb=" O LEU F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 518 Processing helix chain 'F' and resid 538 through 541 No H-bonds generated for 'chain 'F' and resid 538 through 541' Processing helix chain 'F' and resid 548 through 560 removed outlier: 3.529A pdb=" N LEU F 557 " --> pdb=" O GLN F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 589 No H-bonds generated for 'chain 'F' and resid 587 through 589' Processing helix chain 'F' and resid 607 through 610 No H-bonds generated for 'chain 'F' and resid 607 through 610' Processing sheet with id= A, first strand: chain 'A' and resid 442 through 444 removed outlier: 6.479A pdb=" N THR A 475 " --> pdb=" O TRP A 443 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A 159 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 126 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP A 161 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 206 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 162 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 208 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 310 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 380 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE A 313 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY A 382 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 407 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 267 removed outlier: 3.776A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 569 through 571 removed outlier: 3.660A pdb=" N LEU A 622 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU A 649 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE A 620 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 603 through 605 Processing sheet with id= E, first strand: chain 'A' and resid 673 through 675 Processing sheet with id= F, first strand: chain 'F' and resid 442 through 444 removed outlier: 6.479A pdb=" N THR F 475 " --> pdb=" O TRP F 443 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N MET F 123 " --> pdb=" O THR F 478 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR F 159 " --> pdb=" O TYR F 124 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE F 126 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP F 161 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS F 206 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE F 162 " --> pdb=" O LYS F 206 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE F 208 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 310 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE F 380 " --> pdb=" O PHE F 311 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE F 313 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY F 382 " --> pdb=" O PHE F 313 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE F 407 " --> pdb=" O THR F 383 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 264 through 267 removed outlier: 3.776A pdb=" N GLN F 272 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 569 through 571 removed outlier: 3.660A pdb=" N LEU F 622 " --> pdb=" O ILE F 647 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU F 649 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE F 620 " --> pdb=" O GLU F 649 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 603 through 605 Processing sheet with id= J, first strand: chain 'F' and resid 673 through 675 568 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3078 1.32 - 1.45: 4886 1.45 - 1.57: 9980 1.57 - 1.70: 4 1.70 - 1.82: 162 Bond restraints: 18110 Sorted by residual: bond pdb=" C9 LBN A 701 " pdb=" O2 LBN A 701 " ideal model delta sigma weight residual 1.409 1.455 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C9 LBN F 701 " pdb=" O2 LBN F 701 " ideal model delta sigma weight residual 1.409 1.455 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" O2 LBN A 701 " pdb=" P1 LBN A 701 " ideal model delta sigma weight residual 1.650 1.605 0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" O2 LBN F 701 " pdb=" P1 LBN F 701 " ideal model delta sigma weight residual 1.650 1.605 0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" C1 LBN F 701 " pdb=" O1 LBN F 701 " ideal model delta sigma weight residual 1.410 1.453 -0.043 2.00e-02 2.50e+03 4.71e+00 ... (remaining 18105 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.71: 424 105.71 - 112.80: 9590 112.80 - 119.89: 6204 119.89 - 126.97: 8154 126.97 - 134.06: 272 Bond angle restraints: 24644 Sorted by residual: angle pdb=" C GLU E 96 " pdb=" N TYR E 97 " pdb=" CA TYR E 97 " ideal model delta sigma weight residual 120.09 125.58 -5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" C GLU B 96 " pdb=" N TYR B 97 " pdb=" CA TYR B 97 " ideal model delta sigma weight residual 120.09 125.58 -5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" C PHE A 173 " pdb=" N ARG A 174 " pdb=" CA ARG A 174 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C PHE F 173 " pdb=" N ARG F 174 " pdb=" CA ARG F 174 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" CA TYR F 65 " pdb=" CB TYR F 65 " pdb=" CG TYR F 65 " ideal model delta sigma weight residual 113.90 120.26 -6.36 1.80e+00 3.09e-01 1.25e+01 ... (remaining 24639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 10228 26.27 - 52.54: 718 52.54 - 78.81: 84 78.81 - 105.08: 18 105.08 - 131.34: 8 Dihedral angle restraints: 11056 sinusoidal: 4766 harmonic: 6290 Sorted by residual: dihedral pdb=" CA ARG A 174 " pdb=" C ARG A 174 " pdb=" N HIS A 175 " pdb=" CA HIS A 175 " ideal model delta harmonic sigma weight residual 180.00 137.12 42.88 0 5.00e+00 4.00e-02 7.35e+01 dihedral pdb=" CA ARG F 174 " pdb=" C ARG F 174 " pdb=" N HIS F 175 " pdb=" CA HIS F 175 " ideal model delta harmonic sigma weight residual 180.00 137.12 42.88 0 5.00e+00 4.00e-02 7.35e+01 dihedral pdb=" CA GLN F 79 " pdb=" C GLN F 79 " pdb=" N ALA F 80 " pdb=" CA ALA F 80 " ideal model delta harmonic sigma weight residual -180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 11053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2630 0.087 - 0.174: 162 0.174 - 0.261: 2 0.261 - 0.348: 4 0.348 - 0.434: 2 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.50e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.50e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 2797 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 523 " 0.233 2.00e-02 2.50e+03 3.33e-01 1.38e+03 pdb=" CG ASN A 523 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN A 523 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN A 523 " -0.558 2.00e-02 2.50e+03 pdb=" C1 NAG A 706 " 0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 523 " 0.233 2.00e-02 2.50e+03 3.33e-01 1.38e+03 pdb=" CG ASN F 523 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN F 523 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN F 523 " -0.558 2.00e-02 2.50e+03 pdb=" C1 NAG F 706 " 0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 513 " -0.080 2.00e-02 2.50e+03 2.30e-01 6.59e+02 pdb=" CG ASN F 513 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN F 513 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN F 513 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " 0.271 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 201 2.61 - 3.18: 15285 3.18 - 3.75: 26485 3.75 - 4.33: 39855 4.33 - 4.90: 63680 Nonbonded interactions: 145506 Sorted by model distance: nonbonded pdb=" CE2 TYR B 175 " pdb=" CE2 TYR E 175 " model vdw 2.034 3.640 nonbonded pdb=" O GLY B 47 " pdb=" OG SER B 51 " model vdw 2.114 2.440 nonbonded pdb=" O GLY E 47 " pdb=" OG SER E 51 " model vdw 2.114 2.440 nonbonded pdb=" OG SER B 345 " pdb=" O ARG B 348 " model vdw 2.140 2.440 nonbonded pdb=" OG SER E 345 " pdb=" O ARG E 348 " model vdw 2.140 2.440 ... (remaining 145501 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 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.120 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 48.790 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.130 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.006 0.049 18110 Z= 0.396 Angle : 0.747 9.720 24644 Z= 0.417 Chirality : 0.047 0.434 2800 Planarity : 0.005 0.043 3040 Dihedral : 17.271 131.344 6996 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 8.17 % Allowed : 22.27 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.13), residues: 2148 helix: -4.11 (0.09), residues: 974 sheet: -2.26 (0.31), residues: 176 loop : -2.22 (0.17), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.023 0.002 PHE F 407 TYR 0.018 0.002 TYR F 65 ARG 0.002 0.000 ARG F 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 358 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 124 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7001 (p) REVERT: B 128 ILE cc_start: 0.7688 (mt) cc_final: 0.7318 (mm) REVERT: B 142 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.7030 (t) REVERT: B 151 ILE cc_start: 0.7943 (pt) cc_final: 0.7656 (pp) REVERT: B 171 ARG cc_start: 0.4861 (ptm160) cc_final: 0.4443 (mtp180) REVERT: B 172 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4789 (mt) REVERT: B 207 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.3561 (p90) REVERT: B 209 ASN cc_start: 0.6310 (t0) cc_final: 0.5623 (t0) REVERT: B 221 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6924 (mt) REVERT: B 258 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6773 (pp) REVERT: B 261 PRO cc_start: 0.8048 (Cg_exo) cc_final: 0.7826 (Cg_endo) REVERT: B 268 ILE cc_start: 0.8396 (pt) cc_final: 0.8185 (pp) REVERT: B 282 GLU cc_start: 0.7494 (tt0) cc_final: 0.7281 (tp30) REVERT: B 304 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7137 (pp) REVERT: B 308 PHE cc_start: 0.6409 (m-10) cc_final: 0.6126 (m-10) REVERT: B 338 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6244 (tt) REVERT: B 356 MET cc_start: 0.6523 (mmm) cc_final: 0.5969 (mmm) REVERT: B 393 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6411 (tt) REVERT: B 403 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5809 (pt) REVERT: B 454 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.5888 (t80) REVERT: B 473 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 113 LYS cc_start: 0.7929 (mttm) cc_final: 0.7299 (tttm) REVERT: A 250 ILE cc_start: 0.8574 (pp) cc_final: 0.8282 (mm) REVERT: A 426 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7286 (pp20) REVERT: A 433 GLU cc_start: 0.7498 (pt0) cc_final: 0.7272 (pt0) REVERT: A 500 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8656 (m) REVERT: A 589 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (mp) REVERT: E 113 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7868 (p) REVERT: E 124 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7006 (p) REVERT: E 128 ILE cc_start: 0.7686 (mt) cc_final: 0.7317 (mm) REVERT: E 142 SER cc_start: 0.7267 (OUTLIER) cc_final: 0.7027 (t) REVERT: E 151 ILE cc_start: 0.7946 (pt) cc_final: 0.7657 (pp) REVERT: E 171 ARG cc_start: 0.4861 (ptm160) cc_final: 0.4628 (mtt-85) REVERT: E 172 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4789 (mt) REVERT: E 207 PHE cc_start: 0.5388 (OUTLIER) cc_final: 0.3559 (p90) REVERT: E 209 ASN cc_start: 0.6312 (t0) cc_final: 0.5622 (t0) REVERT: E 221 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6928 (mt) REVERT: E 258 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6775 (pp) REVERT: E 261 PRO cc_start: 0.8049 (Cg_exo) cc_final: 0.7826 (Cg_endo) REVERT: E 268 ILE cc_start: 0.8396 (pt) cc_final: 0.8186 (pp) REVERT: E 282 GLU cc_start: 0.7492 (tt0) cc_final: 0.7280 (tp30) REVERT: E 304 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7139 (pp) REVERT: E 308 PHE cc_start: 0.6412 (m-10) cc_final: 0.6128 (m-10) REVERT: E 338 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6240 (tt) REVERT: E 356 MET cc_start: 0.6526 (mmm) cc_final: 0.5973 (mmm) REVERT: E 393 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6413 (tt) REVERT: E 403 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5812 (pt) REVERT: E 454 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5890 (t80) REVERT: E 473 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8051 (mt) REVERT: F 113 LYS cc_start: 0.7926 (mttm) cc_final: 0.7296 (tttm) REVERT: F 250 ILE cc_start: 0.8574 (pp) cc_final: 0.8282 (mm) REVERT: F 426 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7287 (pp20) REVERT: F 433 GLU cc_start: 0.7496 (pt0) cc_final: 0.7271 (pt0) REVERT: F 500 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8656 (m) REVERT: F 589 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7999 (mp) outliers start: 154 outliers final: 24 residues processed: 478 average time/residue: 1.0151 time to fit residues: 554.9742 Evaluate side-chains 282 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 321 CYS Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 454 PHE Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.0070 chunk 124 optimal weight: 1.9990 chunk 194 optimal weight: 0.0770 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN B 203 ASN B 237 GLN B 372 ASN B 456 HIS A 79 GLN A 146 GLN A 181 GLN A 201 HIS A 220 HIS A 224 GLN A 282 GLN A 293 GLN A 301 GLN A 335 GLN A 345 GLN A 366 GLN A 370 GLN A 403 GLN A 442 ASN A 466 ASN A 510 GLN A 544 GLN A 575 ASN A 606 ASN E 148 GLN E 203 ASN E 237 GLN E 372 ASN E 456 HIS F 79 GLN F 146 GLN F 181 GLN F 201 HIS F 220 HIS F 224 GLN F 282 GLN F 293 GLN F 301 GLN F 335 GLN F 345 GLN F 366 GLN F 370 GLN F 403 GLN F 442 ASN F 466 ASN F 510 GLN F 544 GLN F 575 ASN F 606 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18110 Z= 0.196 Angle : 0.703 11.712 24644 Z= 0.349 Chirality : 0.046 0.334 2800 Planarity : 0.005 0.039 3040 Dihedral : 10.657 124.007 3110 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 5.94 % Allowed : 25.34 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.16), residues: 2148 helix: -1.89 (0.14), residues: 972 sheet: -1.76 (0.31), residues: 180 loop : -1.43 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 383 HIS 0.008 0.001 HIS F 175 PHE 0.012 0.001 PHE E 293 TYR 0.017 0.001 TYR A 65 ARG 0.007 0.001 ARG F 671 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 254 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 MET cc_start: 0.6657 (ttm) cc_final: 0.6125 (ttp) REVERT: B 111 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7248 (mp) REVERT: B 128 ILE cc_start: 0.7302 (mt) cc_final: 0.7007 (mm) REVERT: B 175 TYR cc_start: 0.4157 (t80) cc_final: 0.3891 (t80) REVERT: B 185 MET cc_start: 0.6421 (mmm) cc_final: 0.6108 (mmm) REVERT: B 205 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5820 (mtp-110) REVERT: B 209 ASN cc_start: 0.6143 (t0) cc_final: 0.5784 (t0) REVERT: B 233 ASP cc_start: 0.6987 (t70) cc_final: 0.6669 (t70) REVERT: B 238 LEU cc_start: 0.7243 (tp) cc_final: 0.6967 (tp) REVERT: B 258 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6498 (tt) REVERT: B 337 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5468 (ppp) REVERT: B 390 ILE cc_start: 0.7186 (mm) cc_final: 0.6854 (mm) REVERT: B 454 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5840 (t80) REVERT: B 473 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8043 (mp) REVERT: A 113 LYS cc_start: 0.7937 (mttm) cc_final: 0.7267 (tttm) REVERT: A 420 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8361 (p) REVERT: A 423 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8295 (m) REVERT: A 500 THR cc_start: 0.8908 (p) cc_final: 0.8643 (m) REVERT: A 617 ARG cc_start: 0.7931 (ttt90) cc_final: 0.7711 (ttm-80) REVERT: A 639 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7869 (m) REVERT: E 71 MET cc_start: 0.6657 (ttm) cc_final: 0.6127 (ttp) REVERT: E 111 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7250 (mp) REVERT: E 128 ILE cc_start: 0.7300 (mt) cc_final: 0.7005 (mm) REVERT: E 175 TYR cc_start: 0.4162 (t80) cc_final: 0.3895 (t80) REVERT: E 185 MET cc_start: 0.6419 (mmm) cc_final: 0.6106 (mmm) REVERT: E 205 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5820 (mtp-110) REVERT: E 209 ASN cc_start: 0.6143 (t0) cc_final: 0.5782 (t0) REVERT: E 233 ASP cc_start: 0.6987 (t70) cc_final: 0.6668 (t70) REVERT: E 238 LEU cc_start: 0.7249 (tp) cc_final: 0.6973 (tp) REVERT: E 258 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6498 (tt) REVERT: E 337 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5471 (ppp) REVERT: E 390 ILE cc_start: 0.7187 (mm) cc_final: 0.6856 (mm) REVERT: E 454 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5840 (t80) REVERT: E 473 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8042 (mp) REVERT: F 113 LYS cc_start: 0.7937 (mttm) cc_final: 0.7265 (tttm) REVERT: F 420 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8361 (p) REVERT: F 423 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8295 (m) REVERT: F 500 THR cc_start: 0.8909 (p) cc_final: 0.8642 (m) REVERT: F 617 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7714 (ttm-80) REVERT: F 639 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7867 (m) outliers start: 112 outliers final: 26 residues processed: 338 average time/residue: 0.9890 time to fit residues: 385.3981 Evaluate side-chains 250 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 454 PHE Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 587 ASP Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 194 optimal weight: 0.3980 chunk 210 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 251 ASN A 403 GLN A 654 ASN E 237 GLN E 251 ASN F 403 GLN F 654 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18110 Z= 0.223 Angle : 0.667 9.156 24644 Z= 0.327 Chirality : 0.047 0.457 2800 Planarity : 0.005 0.041 3040 Dihedral : 8.975 124.599 3046 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 5.62 % Allowed : 26.62 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.73 (0.17), residues: 2148 helix: -0.87 (0.16), residues: 998 sheet: -1.46 (0.33), residues: 180 loop : -1.25 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 383 HIS 0.007 0.001 HIS F 175 PHE 0.022 0.002 PHE B 249 TYR 0.014 0.001 TYR A 65 ARG 0.006 0.001 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 240 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.6902 (mmp) cc_final: 0.6557 (mmm) REVERT: B 104 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.5509 (t80) REVERT: B 128 ILE cc_start: 0.7291 (mt) cc_final: 0.7059 (mm) REVERT: B 171 ARG cc_start: 0.5023 (ptm160) cc_final: 0.4653 (mtp180) REVERT: B 175 TYR cc_start: 0.4396 (t80) cc_final: 0.4179 (t80) REVERT: B 185 MET cc_start: 0.6284 (mmm) cc_final: 0.5951 (mmm) REVERT: B 207 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.3499 (p90) REVERT: B 233 ASP cc_start: 0.7144 (t70) cc_final: 0.6772 (t70) REVERT: B 250 ARG cc_start: 0.6493 (mmm-85) cc_final: 0.4871 (tmm-80) REVERT: B 326 ARG cc_start: 0.6447 (mmt90) cc_final: 0.6165 (mmt90) REVERT: B 333 ARG cc_start: 0.6451 (mmp80) cc_final: 0.6080 (mmp-170) REVERT: B 337 MET cc_start: 0.6320 (ttp) cc_final: 0.5686 (tmm) REVERT: B 356 MET cc_start: 0.6225 (mtp) cc_final: 0.5941 (mmm) REVERT: B 390 ILE cc_start: 0.6998 (mm) cc_final: 0.6765 (mm) REVERT: B 454 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5710 (t80) REVERT: B 473 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 68 MET cc_start: 0.5967 (mtm) cc_final: 0.5706 (mtm) REVERT: A 113 LYS cc_start: 0.7974 (mttm) cc_final: 0.7585 (tppt) REVERT: A 339 THR cc_start: 0.8894 (p) cc_final: 0.8671 (p) REVERT: A 420 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 423 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8369 (m) REVERT: A 486 MET cc_start: 0.8982 (mtp) cc_final: 0.8764 (mtm) REVERT: A 500 THR cc_start: 0.8928 (p) cc_final: 0.8705 (m) REVERT: A 524 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.6862 (p-80) REVERT: A 617 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7612 (ttm-80) REVERT: A 671 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7726 (ptp90) REVERT: E 59 MET cc_start: 0.6898 (mmp) cc_final: 0.6554 (mmm) REVERT: E 104 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.5511 (t80) REVERT: E 128 ILE cc_start: 0.7286 (mt) cc_final: 0.7055 (mm) REVERT: E 171 ARG cc_start: 0.5027 (ptm160) cc_final: 0.4784 (mtt-85) REVERT: E 175 TYR cc_start: 0.4402 (t80) cc_final: 0.4179 (t80) REVERT: E 185 MET cc_start: 0.6281 (mmm) cc_final: 0.5948 (mmm) REVERT: E 207 PHE cc_start: 0.5386 (OUTLIER) cc_final: 0.3501 (p90) REVERT: E 233 ASP cc_start: 0.7148 (t70) cc_final: 0.6776 (t70) REVERT: E 250 ARG cc_start: 0.6495 (mmm-85) cc_final: 0.4872 (tmm-80) REVERT: E 326 ARG cc_start: 0.6449 (mmt90) cc_final: 0.6165 (mmt90) REVERT: E 333 ARG cc_start: 0.6452 (mmp80) cc_final: 0.6083 (mmp-170) REVERT: E 337 MET cc_start: 0.6320 (ttp) cc_final: 0.5685 (tmm) REVERT: E 356 MET cc_start: 0.6223 (mtp) cc_final: 0.5941 (mmm) REVERT: E 390 ILE cc_start: 0.7002 (mm) cc_final: 0.6769 (mm) REVERT: E 454 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5711 (t80) REVERT: E 473 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8183 (mp) REVERT: F 68 MET cc_start: 0.5964 (mtm) cc_final: 0.5707 (mtm) REVERT: F 113 LYS cc_start: 0.7974 (mttm) cc_final: 0.7585 (tppt) REVERT: F 339 THR cc_start: 0.8896 (p) cc_final: 0.8672 (p) REVERT: F 420 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8214 (p) REVERT: F 423 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8366 (m) REVERT: F 486 MET cc_start: 0.8982 (mtp) cc_final: 0.8766 (mtm) REVERT: F 500 THR cc_start: 0.8928 (p) cc_final: 0.8704 (m) REVERT: F 524 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.6864 (p-80) REVERT: F 617 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7616 (ttm-80) REVERT: F 671 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7727 (ptp90) outliers start: 106 outliers final: 38 residues processed: 314 average time/residue: 1.2688 time to fit residues: 446.4411 Evaluate side-chains 274 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 454 PHE Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 671 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 0.0070 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 474 GLN A 403 GLN E 237 GLN E 474 GLN F 403 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18110 Z= 0.204 Angle : 0.633 8.507 24644 Z= 0.310 Chirality : 0.044 0.329 2800 Planarity : 0.004 0.038 3040 Dihedral : 8.410 125.140 3042 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 4.88 % Allowed : 26.41 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.21 (0.17), residues: 2148 helix: -0.32 (0.17), residues: 966 sheet: -1.33 (0.33), residues: 180 loop : -1.08 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 383 HIS 0.006 0.001 HIS F 175 PHE 0.015 0.001 PHE F 407 TYR 0.017 0.001 TYR A 65 ARG 0.004 0.000 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 240 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.6910 (mmp) cc_final: 0.6610 (mmm) REVERT: B 171 ARG cc_start: 0.5235 (ptm160) cc_final: 0.4696 (mtt-85) REVERT: B 185 MET cc_start: 0.6325 (mmm) cc_final: 0.5977 (mmm) REVERT: B 207 PHE cc_start: 0.5471 (OUTLIER) cc_final: 0.3632 (p90) REVERT: B 233 ASP cc_start: 0.7073 (t70) cc_final: 0.6765 (t70) REVERT: B 250 ARG cc_start: 0.6555 (mmm-85) cc_final: 0.6311 (mmm-85) REVERT: B 333 ARG cc_start: 0.6366 (mmp80) cc_final: 0.5990 (mmp-170) REVERT: B 337 MET cc_start: 0.6324 (ttp) cc_final: 0.6110 (tmm) REVERT: B 356 MET cc_start: 0.6115 (mtp) cc_final: 0.5899 (mmm) REVERT: B 360 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6612 (tmm) REVERT: A 68 MET cc_start: 0.6070 (mtm) cc_final: 0.5860 (mtm) REVERT: A 113 LYS cc_start: 0.8040 (mttm) cc_final: 0.7591 (mttm) REVERT: A 486 MET cc_start: 0.8991 (mtp) cc_final: 0.8623 (mtm) REVERT: A 524 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.6909 (p-80) REVERT: A 617 ARG cc_start: 0.7901 (ttt90) cc_final: 0.7617 (ttm-80) REVERT: A 639 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.8067 (m) REVERT: E 59 MET cc_start: 0.6907 (mmp) cc_final: 0.6606 (mmm) REVERT: E 171 ARG cc_start: 0.5238 (ptm160) cc_final: 0.4852 (ttt-90) REVERT: E 185 MET cc_start: 0.6323 (mmm) cc_final: 0.5974 (mmm) REVERT: E 207 PHE cc_start: 0.5469 (OUTLIER) cc_final: 0.3632 (p90) REVERT: E 233 ASP cc_start: 0.7074 (t70) cc_final: 0.6768 (t70) REVERT: E 250 ARG cc_start: 0.6554 (mmm-85) cc_final: 0.6308 (mmm-85) REVERT: E 333 ARG cc_start: 0.6364 (mmp80) cc_final: 0.5989 (mmp-170) REVERT: E 337 MET cc_start: 0.6319 (ttp) cc_final: 0.6103 (tmm) REVERT: E 356 MET cc_start: 0.6115 (mtp) cc_final: 0.5901 (mmm) REVERT: E 360 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6609 (tmm) REVERT: F 68 MET cc_start: 0.6058 (mtm) cc_final: 0.5852 (mtm) REVERT: F 113 LYS cc_start: 0.8039 (mttm) cc_final: 0.7588 (mttm) REVERT: F 486 MET cc_start: 0.8993 (mtp) cc_final: 0.8626 (mtm) REVERT: F 524 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.6907 (p-80) REVERT: F 617 ARG cc_start: 0.7901 (ttt90) cc_final: 0.7619 (ttm-80) REVERT: F 639 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.8068 (m) outliers start: 92 outliers final: 52 residues processed: 298 average time/residue: 1.3342 time to fit residues: 442.9111 Evaluate side-chains 276 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 216 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 358 HIS B 474 GLN A 403 GLN A 516 ASN E 237 GLN E 358 HIS E 474 GLN F 403 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18110 Z= 0.223 Angle : 0.625 8.192 24644 Z= 0.309 Chirality : 0.044 0.326 2800 Planarity : 0.004 0.036 3040 Dihedral : 8.077 126.235 3034 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 5.73 % Allowed : 26.03 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2148 helix: -0.08 (0.17), residues: 964 sheet: -1.20 (0.34), residues: 180 loop : -1.05 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 114 HIS 0.006 0.001 HIS A 175 PHE 0.018 0.001 PHE B 249 TYR 0.016 0.001 TYR A 65 ARG 0.008 0.001 ARG F 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 220 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 ARG cc_start: 0.5329 (ptm160) cc_final: 0.4769 (mtp180) REVERT: B 185 MET cc_start: 0.6420 (mmm) cc_final: 0.6123 (mmm) REVERT: B 207 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.4010 (p90) REVERT: B 233 ASP cc_start: 0.7085 (t70) cc_final: 0.6830 (t70) REVERT: B 250 ARG cc_start: 0.6543 (mmm-85) cc_final: 0.6141 (mmm-85) REVERT: B 333 ARG cc_start: 0.6438 (mmp80) cc_final: 0.6034 (mmp-170) REVERT: B 337 MET cc_start: 0.6552 (ttp) cc_final: 0.6318 (tmm) REVERT: B 343 TYR cc_start: 0.6267 (m-10) cc_final: 0.6007 (m-80) REVERT: B 361 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6694 (mm) REVERT: B 365 TYR cc_start: 0.7558 (m-80) cc_final: 0.7328 (m-80) REVERT: B 474 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: A 68 MET cc_start: 0.6269 (mtm) cc_final: 0.5274 (mtm) REVERT: A 113 LYS cc_start: 0.8034 (mttm) cc_final: 0.7580 (mttt) REVERT: A 243 ASN cc_start: 0.7756 (t0) cc_final: 0.7480 (t0) REVERT: A 374 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7136 (pt0) REVERT: A 486 MET cc_start: 0.9006 (mtp) cc_final: 0.8635 (mtm) REVERT: A 617 ARG cc_start: 0.7891 (ttt90) cc_final: 0.7618 (ttm-80) REVERT: E 171 ARG cc_start: 0.5330 (ptm160) cc_final: 0.5002 (ttt-90) REVERT: E 185 MET cc_start: 0.6419 (mmm) cc_final: 0.6124 (mmm) REVERT: E 207 PHE cc_start: 0.5620 (OUTLIER) cc_final: 0.4009 (p90) REVERT: E 233 ASP cc_start: 0.7078 (t70) cc_final: 0.6827 (t70) REVERT: E 250 ARG cc_start: 0.6546 (mmm-85) cc_final: 0.6142 (mmm-85) REVERT: E 333 ARG cc_start: 0.6442 (mmp80) cc_final: 0.6035 (mmp-170) REVERT: E 337 MET cc_start: 0.6546 (ttp) cc_final: 0.6310 (tmm) REVERT: E 343 TYR cc_start: 0.6275 (m-10) cc_final: 0.6018 (m-80) REVERT: E 361 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6692 (mm) REVERT: E 365 TYR cc_start: 0.7552 (m-80) cc_final: 0.7320 (m-80) REVERT: E 474 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: F 68 MET cc_start: 0.6258 (mtm) cc_final: 0.5265 (mtm) REVERT: F 113 LYS cc_start: 0.8031 (mttm) cc_final: 0.7577 (mttt) REVERT: F 243 ASN cc_start: 0.7754 (t0) cc_final: 0.7480 (t0) REVERT: F 374 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: F 486 MET cc_start: 0.9006 (mtp) cc_final: 0.8635 (mtm) REVERT: F 617 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7621 (ttm-80) outliers start: 108 outliers final: 56 residues processed: 292 average time/residue: 1.3832 time to fit residues: 449.6327 Evaluate side-chains 270 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 206 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.9980 chunk 186 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN E 237 GLN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN F 516 ASN F 670 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18110 Z= 0.188 Angle : 0.613 8.686 24644 Z= 0.300 Chirality : 0.043 0.325 2800 Planarity : 0.004 0.037 3040 Dihedral : 7.972 125.972 3034 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 5.41 % Allowed : 26.41 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.81 (0.18), residues: 2148 helix: 0.10 (0.17), residues: 954 sheet: -1.05 (0.35), residues: 180 loop : -0.98 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 114 HIS 0.007 0.001 HIS F 175 PHE 0.015 0.001 PHE A 407 TYR 0.017 0.001 TYR A 65 ARG 0.008 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 210 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 ARG cc_start: 0.5364 (ptm160) cc_final: 0.4766 (mtp180) REVERT: B 185 MET cc_start: 0.6435 (mmm) cc_final: 0.6125 (mmm) REVERT: B 233 ASP cc_start: 0.7095 (t70) cc_final: 0.6813 (t70) REVERT: B 250 ARG cc_start: 0.6448 (mmm-85) cc_final: 0.4793 (tmm-80) REVERT: B 333 ARG cc_start: 0.6468 (mmp80) cc_final: 0.6066 (mmp-170) REVERT: B 337 MET cc_start: 0.6530 (ttp) cc_final: 0.6261 (tmm) REVERT: B 343 TYR cc_start: 0.6179 (m-10) cc_final: 0.5816 (m-80) REVERT: B 365 TYR cc_start: 0.7541 (m-80) cc_final: 0.7296 (m-80) REVERT: B 397 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6977 (mmm160) REVERT: B 475 MET cc_start: 0.7989 (mtm) cc_final: 0.7589 (ptt) REVERT: A 68 MET cc_start: 0.6041 (mtm) cc_final: 0.5345 (mtm) REVERT: A 113 LYS cc_start: 0.8074 (mttm) cc_final: 0.7586 (mttt) REVERT: A 374 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7050 (pt0) REVERT: A 486 MET cc_start: 0.9000 (mtp) cc_final: 0.8621 (mtm) REVERT: A 521 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: A 524 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.6967 (p-80) REVERT: A 617 ARG cc_start: 0.7785 (ttt90) cc_final: 0.7539 (ttm-80) REVERT: E 171 ARG cc_start: 0.5365 (ptm160) cc_final: 0.5002 (ttt-90) REVERT: E 185 MET cc_start: 0.6434 (mmm) cc_final: 0.6125 (mmm) REVERT: E 233 ASP cc_start: 0.7085 (t70) cc_final: 0.6807 (t70) REVERT: E 250 ARG cc_start: 0.6448 (mmm-85) cc_final: 0.4793 (tmm-80) REVERT: E 333 ARG cc_start: 0.6470 (mmp80) cc_final: 0.6067 (mmp-170) REVERT: E 343 TYR cc_start: 0.6194 (m-10) cc_final: 0.5825 (m-80) REVERT: E 365 TYR cc_start: 0.7534 (m-80) cc_final: 0.7290 (m-80) REVERT: E 397 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6975 (mmm160) REVERT: E 475 MET cc_start: 0.7987 (mtm) cc_final: 0.7583 (ptt) REVERT: F 68 MET cc_start: 0.6038 (mtm) cc_final: 0.5341 (mtm) REVERT: F 113 LYS cc_start: 0.8073 (mttm) cc_final: 0.7584 (mttt) REVERT: F 374 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: F 486 MET cc_start: 0.9000 (mtp) cc_final: 0.8622 (mtm) REVERT: F 521 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6508 (tp30) REVERT: F 524 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.6967 (p-80) REVERT: F 617 ARG cc_start: 0.7785 (ttt90) cc_final: 0.7540 (ttm-80) outliers start: 102 outliers final: 59 residues processed: 280 average time/residue: 1.3705 time to fit residues: 426.5455 Evaluate side-chains 275 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 208 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 521 GLU Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 237 GLN B 474 GLN A 403 GLN E 58 ASN E 237 GLN E 474 GLN F 403 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18110 Z= 0.293 Angle : 0.648 8.987 24644 Z= 0.319 Chirality : 0.045 0.327 2800 Planarity : 0.005 0.113 3040 Dihedral : 8.118 127.004 3034 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 5.25 % Allowed : 26.41 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.81 (0.18), residues: 2148 helix: 0.11 (0.17), residues: 970 sheet: -1.13 (0.34), residues: 190 loop : -0.98 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 114 HIS 0.006 0.001 HIS A 348 PHE 0.020 0.002 PHE F 407 TYR 0.017 0.001 TYR F 259 ARG 0.010 0.001 ARG F 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 211 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 ARG cc_start: 0.5080 (ptm160) cc_final: 0.4625 (ttt-90) REVERT: B 207 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.4472 (p90) REVERT: B 233 ASP cc_start: 0.7093 (t70) cc_final: 0.6838 (t70) REVERT: B 238 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6808 (tp) REVERT: B 250 ARG cc_start: 0.6435 (mmm-85) cc_final: 0.4773 (tmm-80) REVERT: B 333 ARG cc_start: 0.6466 (mmp80) cc_final: 0.6175 (mmp-170) REVERT: B 337 MET cc_start: 0.6576 (ttp) cc_final: 0.6221 (tmm) REVERT: B 343 TYR cc_start: 0.6246 (m-10) cc_final: 0.5797 (m-80) REVERT: B 396 MET cc_start: 0.6411 (ptp) cc_final: 0.6137 (ptm) REVERT: B 415 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7027 (tp) REVERT: B 475 MET cc_start: 0.7990 (mtm) cc_final: 0.7061 (tpt) REVERT: A 68 MET cc_start: 0.6200 (mtm) cc_final: 0.5594 (mtm) REVERT: A 113 LYS cc_start: 0.8070 (mttm) cc_final: 0.7566 (mttt) REVERT: A 374 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: A 486 MET cc_start: 0.9026 (mtp) cc_final: 0.8654 (mtm) REVERT: A 617 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7580 (ttm-80) REVERT: E 171 ARG cc_start: 0.5080 (ptm160) cc_final: 0.4625 (ttt-90) REVERT: E 207 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.4466 (p90) REVERT: E 233 ASP cc_start: 0.7087 (t70) cc_final: 0.6838 (t70) REVERT: E 238 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6818 (tp) REVERT: E 250 ARG cc_start: 0.6434 (mmm-85) cc_final: 0.4772 (tmm-80) REVERT: E 333 ARG cc_start: 0.6465 (mmp80) cc_final: 0.6161 (mmp-170) REVERT: E 337 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5891 (tmm) REVERT: E 343 TYR cc_start: 0.6278 (m-10) cc_final: 0.5827 (m-80) REVERT: E 396 MET cc_start: 0.6411 (ptp) cc_final: 0.6138 (ptm) REVERT: E 415 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7024 (tp) REVERT: E 475 MET cc_start: 0.7989 (mtm) cc_final: 0.7058 (tpt) REVERT: F 68 MET cc_start: 0.6196 (mtm) cc_final: 0.5589 (mtm) REVERT: F 113 LYS cc_start: 0.8057 (mttm) cc_final: 0.7569 (mttt) REVERT: F 374 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: F 486 MET cc_start: 0.9027 (mtp) cc_final: 0.8657 (mtm) REVERT: F 617 ARG cc_start: 0.7828 (ttt90) cc_final: 0.7581 (ttm-80) outliers start: 99 outliers final: 62 residues processed: 283 average time/residue: 1.3000 time to fit residues: 411.0520 Evaluate side-chains 271 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 200 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 658 ARG Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 0.0570 chunk 123 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 chunk 162 optimal weight: 0.0770 chunk 187 optimal weight: 0.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN A 403 GLN E 237 GLN F 156 ASN F 403 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18110 Z= 0.156 Angle : 0.608 8.806 24644 Z= 0.295 Chirality : 0.043 0.322 2800 Planarity : 0.004 0.038 3040 Dihedral : 7.897 125.432 3034 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 3.92 % Allowed : 27.73 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2148 helix: 0.34 (0.17), residues: 958 sheet: -0.90 (0.36), residues: 180 loop : -0.90 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 114 HIS 0.008 0.001 HIS F 175 PHE 0.011 0.001 PHE F 173 TYR 0.017 0.001 TYR A 65 ARG 0.009 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 212 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 THR cc_start: 0.5705 (m) cc_final: 0.5358 (p) REVERT: B 171 ARG cc_start: 0.5127 (ptm160) cc_final: 0.4745 (ttt-90) REVERT: B 185 MET cc_start: 0.6468 (mmm) cc_final: 0.6043 (mmm) REVERT: B 233 ASP cc_start: 0.7023 (t70) cc_final: 0.6774 (t70) REVERT: B 238 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6801 (tp) REVERT: B 250 ARG cc_start: 0.6454 (mmm-85) cc_final: 0.4834 (tmm-80) REVERT: B 283 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6667 (tt) REVERT: B 333 ARG cc_start: 0.6349 (mmp80) cc_final: 0.6097 (mmp-170) REVERT: B 337 MET cc_start: 0.6695 (ttp) cc_final: 0.6340 (tmm) REVERT: B 343 TYR cc_start: 0.6260 (m-10) cc_final: 0.5830 (m-80) REVERT: B 365 TYR cc_start: 0.7402 (m-80) cc_final: 0.7201 (m-80) REVERT: B 397 ARG cc_start: 0.7187 (mmm-85) cc_final: 0.6899 (mmm-85) REVERT: B 415 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6991 (tp) REVERT: A 68 MET cc_start: 0.6270 (mtm) cc_final: 0.5588 (mtm) REVERT: A 113 LYS cc_start: 0.8086 (mttm) cc_final: 0.7585 (mttt) REVERT: A 486 MET cc_start: 0.8998 (mtp) cc_final: 0.8613 (mtm) REVERT: A 521 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6436 (tp30) REVERT: A 524 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.6978 (p-80) REVERT: E 77 THR cc_start: 0.5705 (m) cc_final: 0.5358 (p) REVERT: E 171 ARG cc_start: 0.5125 (ptm160) cc_final: 0.4745 (ttt-90) REVERT: E 185 MET cc_start: 0.6470 (mmm) cc_final: 0.6045 (mmm) REVERT: E 233 ASP cc_start: 0.7020 (t70) cc_final: 0.6774 (t70) REVERT: E 238 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6811 (tp) REVERT: E 250 ARG cc_start: 0.6451 (mmm-85) cc_final: 0.4831 (tmm-80) REVERT: E 283 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6674 (tt) REVERT: E 333 ARG cc_start: 0.6390 (mmp80) cc_final: 0.6124 (mmp-170) REVERT: E 337 MET cc_start: 0.6165 (tmm) cc_final: 0.5824 (tmm) REVERT: E 343 TYR cc_start: 0.6302 (m-10) cc_final: 0.5852 (m-80) REVERT: E 365 TYR cc_start: 0.7397 (m-80) cc_final: 0.7194 (m-80) REVERT: E 397 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6900 (mmm-85) REVERT: E 415 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6986 (tp) REVERT: F 68 MET cc_start: 0.6266 (mtm) cc_final: 0.5585 (mtm) REVERT: F 113 LYS cc_start: 0.8086 (mttm) cc_final: 0.7588 (mttt) REVERT: F 486 MET cc_start: 0.8992 (mtp) cc_final: 0.8606 (mtm) REVERT: F 521 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6444 (tp30) outliers start: 74 outliers final: 42 residues processed: 270 average time/residue: 1.4074 time to fit residues: 423.7990 Evaluate side-chains 251 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 521 GLU Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN A 403 GLN E 237 GLN F 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18110 Z= 0.203 Angle : 0.625 8.507 24644 Z= 0.302 Chirality : 0.043 0.326 2800 Planarity : 0.004 0.037 3040 Dihedral : 7.836 125.160 3034 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 3.87 % Allowed : 28.26 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.45 (0.18), residues: 2148 helix: 0.47 (0.18), residues: 948 sheet: -0.94 (0.36), residues: 180 loop : -0.84 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 114 HIS 0.006 0.001 HIS A 175 PHE 0.019 0.001 PHE B 249 TYR 0.016 0.001 TYR F 259 ARG 0.009 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 199 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 THR cc_start: 0.5775 (m) cc_final: 0.5469 (p) REVERT: B 171 ARG cc_start: 0.5021 (ptm160) cc_final: 0.4634 (ttt-90) REVERT: B 233 ASP cc_start: 0.7021 (t70) cc_final: 0.6779 (t70) REVERT: B 238 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6820 (tp) REVERT: B 250 ARG cc_start: 0.6370 (mmm-85) cc_final: 0.4899 (tmm-80) REVERT: B 283 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6727 (tt) REVERT: B 333 ARG cc_start: 0.6400 (mmp80) cc_final: 0.6140 (mmp-170) REVERT: B 337 MET cc_start: 0.6715 (ttp) cc_final: 0.6129 (tmm) REVERT: B 343 TYR cc_start: 0.6229 (m-10) cc_final: 0.5751 (m-80) REVERT: B 397 ARG cc_start: 0.7089 (mmm-85) cc_final: 0.6809 (mmm-85) REVERT: B 415 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6984 (tp) REVERT: A 68 MET cc_start: 0.6441 (mtm) cc_final: 0.5739 (mtm) REVERT: A 486 MET cc_start: 0.9019 (mtp) cc_final: 0.8632 (mtm) REVERT: A 521 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6442 (tp30) REVERT: E 77 THR cc_start: 0.5781 (m) cc_final: 0.5473 (p) REVERT: E 171 ARG cc_start: 0.5021 (ptm160) cc_final: 0.4634 (ttt-90) REVERT: E 233 ASP cc_start: 0.7019 (t70) cc_final: 0.6777 (t70) REVERT: E 238 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6831 (tp) REVERT: E 250 ARG cc_start: 0.6369 (mmm-85) cc_final: 0.4899 (tmm-80) REVERT: E 283 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6728 (tt) REVERT: E 333 ARG cc_start: 0.6397 (mmp80) cc_final: 0.6125 (mmp-170) REVERT: E 337 MET cc_start: 0.6226 (tmm) cc_final: 0.5948 (tmm) REVERT: E 343 TYR cc_start: 0.6225 (m-10) cc_final: 0.5763 (m-80) REVERT: E 397 ARG cc_start: 0.7088 (mmm-85) cc_final: 0.6809 (mmm-85) REVERT: E 415 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6981 (tp) REVERT: F 68 MET cc_start: 0.6433 (mtm) cc_final: 0.5733 (mtm) REVERT: F 486 MET cc_start: 0.9021 (mtp) cc_final: 0.8638 (mtm) REVERT: F 521 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6445 (tp30) REVERT: F 524 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6971 (p-80) outliers start: 73 outliers final: 48 residues processed: 259 average time/residue: 1.4054 time to fit residues: 403.5496 Evaluate side-chains 251 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 194 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 521 GLU Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 3.9990 chunk 124 optimal weight: 0.0870 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 196 optimal weight: 0.4980 chunk 169 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 403 GLN F 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18110 Z= 0.165 Angle : 0.607 8.472 24644 Z= 0.295 Chirality : 0.043 0.326 2800 Planarity : 0.004 0.037 3040 Dihedral : 7.699 124.051 3034 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 3.08 % Allowed : 29.22 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.38 (0.18), residues: 2148 helix: 0.53 (0.18), residues: 948 sheet: -0.90 (0.36), residues: 180 loop : -0.81 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 114 HIS 0.007 0.001 HIS F 175 PHE 0.012 0.001 PHE E 132 TYR 0.016 0.001 TYR A 65 ARG 0.009 0.001 ARG A 671 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 208 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.7190 (mmp) cc_final: 0.6824 (mmp) REVERT: B 77 THR cc_start: 0.5796 (m) cc_final: 0.5471 (p) REVERT: B 171 ARG cc_start: 0.5158 (ptm160) cc_final: 0.4748 (ttt-90) REVERT: B 233 ASP cc_start: 0.7097 (t70) cc_final: 0.6882 (t70) REVERT: B 238 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6842 (tp) REVERT: B 250 ARG cc_start: 0.6365 (mmm-85) cc_final: 0.4892 (tmm-80) REVERT: B 283 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6622 (tt) REVERT: B 333 ARG cc_start: 0.6411 (mmp80) cc_final: 0.6163 (mmp-170) REVERT: B 337 MET cc_start: 0.6732 (ttp) cc_final: 0.6117 (tmm) REVERT: B 343 TYR cc_start: 0.6248 (m-10) cc_final: 0.5840 (m-80) REVERT: B 365 TYR cc_start: 0.7367 (m-80) cc_final: 0.6958 (m-80) REVERT: B 397 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6874 (mmm-85) REVERT: B 415 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.6964 (tp) REVERT: A 68 MET cc_start: 0.6414 (mtm) cc_final: 0.5689 (mtm) REVERT: A 113 LYS cc_start: 0.8144 (mttp) cc_final: 0.7720 (mttm) REVERT: A 486 MET cc_start: 0.8996 (mtp) cc_final: 0.8612 (mtm) REVERT: E 59 MET cc_start: 0.7191 (mmp) cc_final: 0.6826 (mmp) REVERT: E 77 THR cc_start: 0.5799 (m) cc_final: 0.5473 (p) REVERT: E 171 ARG cc_start: 0.5155 (ptm160) cc_final: 0.4745 (ttt-90) REVERT: E 233 ASP cc_start: 0.7096 (t70) cc_final: 0.6882 (t70) REVERT: E 238 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6842 (tp) REVERT: E 250 ARG cc_start: 0.6365 (mmm-85) cc_final: 0.4892 (tmm-80) REVERT: E 283 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6632 (tt) REVERT: E 333 ARG cc_start: 0.6483 (mmp80) cc_final: 0.6214 (mmp-170) REVERT: E 337 MET cc_start: 0.6216 (tmm) cc_final: 0.5937 (tmm) REVERT: E 343 TYR cc_start: 0.6236 (m-10) cc_final: 0.5758 (m-80) REVERT: E 365 TYR cc_start: 0.7357 (m-80) cc_final: 0.6945 (m-80) REVERT: E 397 ARG cc_start: 0.7146 (mmm-85) cc_final: 0.6847 (mmm-85) REVERT: E 415 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6961 (tp) REVERT: F 68 MET cc_start: 0.6406 (mtm) cc_final: 0.5687 (mtm) REVERT: F 113 LYS cc_start: 0.8148 (mttp) cc_final: 0.7724 (mttm) REVERT: F 486 MET cc_start: 0.8999 (mtp) cc_final: 0.8615 (mtm) outliers start: 58 outliers final: 46 residues processed: 254 average time/residue: 1.4304 time to fit residues: 402.1208 Evaluate side-chains 254 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 202 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 613 ASN A 654 ASN A 659 GLN F 403 GLN F 613 ASN F 654 ASN F 659 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106117 restraints weight = 20809.951| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.55 r_work: 0.2945 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18110 Z= 0.211 Angle : 0.619 8.425 24644 Z= 0.301 Chirality : 0.044 0.330 2800 Planarity : 0.004 0.037 3040 Dihedral : 7.718 124.049 3034 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 3.66 % Allowed : 28.37 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.38 (0.18), residues: 2148 helix: 0.55 (0.18), residues: 948 sheet: -0.89 (0.37), residues: 180 loop : -0.83 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 114 HIS 0.007 0.001 HIS A 175 PHE 0.018 0.001 PHE F 407 TYR 0.015 0.001 TYR F 259 ARG 0.008 0.001 ARG A 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7398.24 seconds wall clock time: 132 minutes 17.97 seconds (7937.97 seconds total)