Starting phenix.real_space_refine on Sat Mar 23 08:36:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/03_2024/6hz4_0310_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/03_2024/6hz4_0310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/03_2024/6hz4_0310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/03_2024/6hz4_0310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/03_2024/6hz4_0310_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/03_2024/6hz4_0310_trim.pdb" } resolution = 3.6 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= 0.001 sd= 0.011 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: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 3 5.21 5 S 84 5.16 5 C 11750 2.51 5 N 3084 2.21 5 O 3439 1.98 5 H 17933 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 226": not complete - not flipped Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 365": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 226": not complete - not flipped Residue "E ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E GLU 391": "OE1" <-> "OE2" Residue "E ARG 404": not complete - not flipped Residue "E GLU 415": "OE1" <-> "OE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 374": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "M TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 191": "OE1" <-> "OE2" Residue "M GLU 194": "OE1" <-> "OE2" Residue "M GLU 196": "OE1" <-> "OE2" Residue "M ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M GLU 331": "OE1" <-> "OE2" Residue "M GLU 338": "OE1" <-> "OE2" Residue "N GLU 194": "OE1" <-> "OE2" Residue "N ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 338": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36308 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4720 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4719 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "C" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4717 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "D" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4633 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "E" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4637 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "F" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "M" Number of atoms: 5538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5538 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 323} Chain breaks: 2 Chain: "N" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2517 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.42, per 1000 atoms: 0.45 Number of scatterers: 36308 At special positions: 0 Unit cell: (129.15, 115.5, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 84 16.00 P 15 15.00 Mg 3 11.99 O 3439 8.00 N 3084 7.00 C 11750 6.00 H 17933 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.58 Conformation dependent library (CDL) restraints added in 3.5 seconds 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4156 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 19 sheets defined 52.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 169 through 175 removed outlier: 3.755A pdb=" N ALA A 173 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 195 removed outlier: 3.562A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.708A pdb=" N ARG A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 257 through 269 removed outlier: 3.773A pdb=" N GLU A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.563A pdb=" N VAL A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.224A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 298 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.900A pdb=" N ARG A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.661A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 395 removed outlier: 3.854A pdb=" N GLU A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.895A pdb=" N CYS A 411 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 412' Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.540A pdb=" N GLN A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A 451 " --> pdb=" O LYS A 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.685A pdb=" N ILE B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 220 removed outlier: 3.707A pdb=" N ARG B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.769A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.515A pdb=" N ARG B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 removed outlier: 3.661A pdb=" N PHE B 367 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 395 removed outlier: 3.900A pdb=" N GLU B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.672A pdb=" N CYS B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 444 through 457 removed outlier: 3.956A pdb=" N GLN B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 4.094A pdb=" N ALA C 173 " --> pdb=" O CYS C 169 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 195 Processing helix chain 'C' and resid 206 through 220 removed outlier: 3.821A pdb=" N ARG C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 257 through 269 removed outlier: 3.623A pdb=" N GLN C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.717A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.894A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 371 removed outlier: 3.524A pdb=" N ARG C 365 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 371 " --> pdb=" O PHE C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 395 removed outlier: 3.521A pdb=" N GLU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 421 through 432 removed outlier: 3.559A pdb=" N MET C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 441 Processing helix chain 'C' and resid 444 through 457 removed outlier: 3.666A pdb=" N GLN C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 195 Processing helix chain 'D' and resid 206 through 220 Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 257 through 269 removed outlier: 3.671A pdb=" N GLN D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.905A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 345 through 350 removed outlier: 3.505A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.626A pdb=" N ARG D 365 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 393 removed outlier: 3.573A pdb=" N GLU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 removed outlier: 4.028A pdb=" N CYS D 411 " --> pdb=" O HIS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 432 through 441 removed outlier: 3.886A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 457 removed outlier: 3.555A pdb=" N LEU D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 195 removed outlier: 3.561A pdb=" N LEU E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 220 Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 257 through 269 removed outlier: 3.947A pdb=" N GLU E 268 " --> pdb=" O GLN E 264 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN E 269 " --> pdb=" O GLN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 291 Processing helix chain 'E' and resid 292 through 297 removed outlier: 4.351A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 343 through 350 removed outlier: 3.585A pdb=" N ARG E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.568A pdb=" N ARG E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 395 removed outlier: 3.647A pdb=" N GLU E 395 " --> pdb=" O GLU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 407 through 412 removed outlier: 3.655A pdb=" N CYS E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 407 through 412' Processing helix chain 'E' and resid 421 through 432 Processing helix chain 'E' and resid 432 through 442 Processing helix chain 'E' and resid 444 through 457 Processing helix chain 'F' and resid 180 through 195 Processing helix chain 'F' and resid 206 through 220 Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 258 through 269 removed outlier: 3.846A pdb=" N GLU F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 291 Processing helix chain 'F' and resid 292 through 295 removed outlier: 3.635A pdb=" N MET F 295 " --> pdb=" O GLU F 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 292 through 295' Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 343 through 350 removed outlier: 3.546A pdb=" N ARG F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG F 349 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 371 Processing helix chain 'F' and resid 374 through 395 removed outlier: 3.562A pdb=" N LEU F 388 " --> pdb=" O LYS F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 421 through 432 removed outlier: 4.375A pdb=" N GLU F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE F 428 " --> pdb=" O TRP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.643A pdb=" N LEU F 436 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 457 removed outlier: 3.616A pdb=" N GLN F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU F 455 " --> pdb=" O TRP F 451 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 19 removed outlier: 3.685A pdb=" N ILE M 11 " --> pdb=" O PRO M 7 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR M 13 " --> pdb=" O ARG M 9 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET M 14 " --> pdb=" O ASN M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 57 removed outlier: 3.719A pdb=" N LEU M 51 " --> pdb=" O ASN M 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG M 56 " --> pdb=" O GLN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 84 Processing helix chain 'M' and resid 103 through 119 removed outlier: 3.598A pdb=" N ILE M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 137 Processing helix chain 'M' and resid 146 through 153 removed outlier: 3.917A pdb=" N PHE M 150 " --> pdb=" O THR M 146 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 156 No H-bonds generated for 'chain 'M' and resid 154 through 156' Processing helix chain 'M' and resid 161 through 175 removed outlier: 3.649A pdb=" N VAL M 165 " --> pdb=" O TYR M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 213 removed outlier: 3.572A pdb=" N MET M 197 " --> pdb=" O ASN M 193 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG M 210 " --> pdb=" O TYR M 206 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG M 211 " --> pdb=" O GLU M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 266 Processing helix chain 'M' and resid 277 through 289 removed outlier: 4.184A pdb=" N GLN M 281 " --> pdb=" O GLN M 277 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN M 284 " --> pdb=" O TYR M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 331 through 348 Processing helix chain 'N' and resid 194 through 213 Processing helix chain 'N' and resid 261 through 266 removed outlier: 3.858A pdb=" N PHE N 265 " --> pdb=" O TYR N 261 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER N 266 " --> pdb=" O LYS N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 261 through 266' Processing helix chain 'N' and resid 278 through 289 removed outlier: 3.625A pdb=" N ASN N 284 " --> pdb=" O TYR N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 348 removed outlier: 3.568A pdb=" N ASP N 341 " --> pdb=" O GLN N 337 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE N 342 " --> pdb=" O GLU N 338 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS N 348 " --> pdb=" O ASP N 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 231 removed outlier: 6.634A pdb=" N ASN A 228 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASP A 279 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 230 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 197 " --> pdb=" O GLY A 330 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N MET A 332 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU A 199 " --> pdb=" O MET A 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 247 Processing sheet with id=AA3, first strand: chain 'B' and resid 227 through 231 removed outlier: 6.452A pdb=" N ASN B 228 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP B 279 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 230 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 201 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.711A pdb=" N VAL B 308 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 227 through 231 removed outlier: 6.541A pdb=" N ASN C 228 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP C 279 " --> pdb=" O ASN C 228 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 230 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY C 201 " --> pdb=" O MET C 332 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN C 196 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE C 353 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE C 198 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 243 through 247 removed outlier: 3.672A pdb=" N GLY C 244 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 228 through 231 removed outlier: 6.366A pdb=" N ASN D 228 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASP D 279 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 230 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE D 276 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU D 331 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 278 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASN D 333 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN D 196 " --> pdb=" O SER D 351 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE D 353 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE D 198 " --> pdb=" O ILE D 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 245 through 247 Processing sheet with id=AB1, first strand: chain 'E' and resid 228 through 231 removed outlier: 6.855A pdb=" N ASN E 228 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASP E 279 " --> pdb=" O ASN E 228 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL E 230 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR E 274 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE E 329 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE E 276 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU E 331 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 278 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER E 351 " --> pdb=" O ASN E 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 243 through 247 Processing sheet with id=AB3, first strand: chain 'F' and resid 227 through 231 removed outlier: 6.574A pdb=" N ASN F 228 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASP F 279 " --> pdb=" O ASN F 228 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL F 230 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASN F 196 " --> pdb=" O SER F 351 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE F 353 " --> pdb=" O ASN F 196 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE F 198 " --> pdb=" O ILE F 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 243 through 247 Processing sheet with id=AB5, first strand: chain 'F' and resid 308 through 309 removed outlier: 3.556A pdb=" N VAL F 308 " --> pdb=" O PHE F 320 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 61 through 69 removed outlier: 3.999A pdb=" N ASN M 100 " --> pdb=" O ASP M 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 176 through 178 Processing sheet with id=AB8, first strand: chain 'M' and resid 217 through 219 removed outlier: 3.669A pdb=" N LEU M 254 " --> pdb=" O ILE M 247 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE M 302 " --> pdb=" O ASP M 257 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP M 320 " --> pdb=" O ILE M 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 217 through 219 removed outlier: 3.901A pdb=" N ASN N 217 " --> pdb=" O ARG N 248 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP N 320 " --> pdb=" O ILE N 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 222 through 223 removed outlier: 4.612A pdb=" N MET N 241 " --> pdb=" O LEU N 223 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2190 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: 14.64 Time building geometry restraints manager: 31.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17900 1.03 - 1.22: 45 1.22 - 1.42: 8039 1.42 - 1.62: 10623 1.62 - 1.81: 134 Bond restraints: 36741 Sorted by residual: bond pdb=" N3B GNP C1001 " pdb=" PG GNP C1001 " ideal model delta sigma weight residual 1.801 1.466 0.335 2.00e-02 2.50e+03 2.80e+02 bond pdb=" N3B GNP A1001 " pdb=" PG GNP A1001 " ideal model delta sigma weight residual 1.801 1.534 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" N3B GNP B1001 " pdb=" PG GNP B1001 " ideal model delta sigma weight residual 1.801 1.546 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" N3B GNP C1001 " pdb=" PB GNP C1001 " ideal model delta sigma weight residual 1.681 1.447 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" N3B GNP B1001 " pdb=" PB GNP B1001 " ideal model delta sigma weight residual 1.681 1.456 0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 36736 not shown) Histogram of bond angle deviations from ideal: 95.10 - 103.17: 182 103.17 - 111.24: 38511 111.24 - 119.31: 11665 119.31 - 127.38: 15709 127.38 - 135.45: 204 Bond angle restraints: 66271 Sorted by residual: angle pdb=" O3A GNP A1001 " pdb=" PA GNP A1001 " pdb=" O5' GNP A1001 " ideal model delta sigma weight residual 97.31 111.91 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O1A GNP B1001 " pdb=" PA GNP B1001 " pdb=" O2A GNP B1001 " ideal model delta sigma weight residual 121.48 107.34 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" O3A GNP C1001 " pdb=" PA GNP C1001 " pdb=" O5' GNP C1001 " ideal model delta sigma weight residual 97.31 111.15 -13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O3A GNP B1001 " pdb=" PA GNP B1001 " pdb=" O5' GNP B1001 " ideal model delta sigma weight residual 97.31 111.07 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" O1A GNP C1001 " pdb=" PA GNP C1001 " pdb=" O2A GNP C1001 " ideal model delta sigma weight residual 121.48 108.78 12.70 3.00e+00 1.11e-01 1.79e+01 ... (remaining 66266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 16883 35.92 - 71.85: 424 71.85 - 107.77: 14 107.77 - 143.69: 1 143.69 - 179.62: 6 Dihedral angle restraints: 17328 sinusoidal: 9457 harmonic: 7871 Sorted by residual: dihedral pdb=" CD ARG A 226 " pdb=" NE ARG A 226 " pdb=" CZ ARG A 226 " pdb=" NH1 ARG A 226 " ideal model delta sinusoidal sigma weight residual 0.00 -179.62 179.62 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG E 404 " pdb=" NE ARG E 404 " pdb=" CZ ARG E 404 " pdb=" NH1 ARG E 404 " ideal model delta sinusoidal sigma weight residual 0.00 179.62 -179.62 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG E 226 " pdb=" NE ARG E 226 " pdb=" CZ ARG E 226 " pdb=" NH1 ARG E 226 " ideal model delta sinusoidal sigma weight residual 0.00 179.55 -179.55 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 17325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2086 0.066 - 0.131: 528 0.131 - 0.197: 67 0.197 - 0.263: 10 0.263 - 0.328: 2 Chirality restraints: 2693 Sorted by residual: chirality pdb=" C4' GNP A1001 " pdb=" C3' GNP A1001 " pdb=" C5' GNP A1001 " pdb=" O4' GNP A1001 " both_signs ideal model delta sigma weight residual False -2.44 -2.77 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C4' GDP F1001 " pdb=" C5' GDP F1001 " pdb=" O4' GDP F1001 " pdb=" C3' GDP F1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C4' GDP D1001 " pdb=" C5' GDP D1001 " pdb=" O4' GDP D1001 " pdb=" C3' GDP D1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2690 not shown) Planarity restraints: 5372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 243 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLN C 243 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN C 243 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY C 244 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 322 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO C 323 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 323 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 323 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 243 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C GLN E 243 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN E 243 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY E 244 " -0.014 2.00e-02 2.50e+03 ... (remaining 5369 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 3253 2.22 - 2.81: 79497 2.81 - 3.41: 92938 3.41 - 4.00: 126863 4.00 - 4.60: 202809 Nonbonded interactions: 505360 Sorted by model distance: nonbonded pdb=" O PRO A 357 " pdb=" HD1 HIS A 407 " model vdw 1.623 1.850 nonbonded pdb=" H ASN A 248 " pdb=" O GLY A 251 " model vdw 1.631 1.850 nonbonded pdb=" O PRO C 357 " pdb=" HD1 HIS C 407 " model vdw 1.638 1.850 nonbonded pdb="HH12 ARG C 246 " pdb=" O GLY M 74 " model vdw 1.648 1.850 nonbonded pdb=" OE1 GLN D 225 " pdb=" H GLN D 225 " model vdw 1.651 1.850 ... (remaining 505355 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' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 271 or (resid 272 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 throu \ gh 403 or (resid 404 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or n \ ame HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 408 through 453 or (resid 454 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE or name NZ or name H or name HA or name H \ B2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or na \ me HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'B' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 453 or (resid \ 454 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ2)) or res \ id 455 through 457)) selection = (chain 'C' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'D' and (resid 174 through 207 or (resid 208 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 209 through 225 or (resid 22 \ 6 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 \ or name HH12)) or resid 227 through 383 or (resid 384 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name CE or name NZ or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or nam \ e HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name ND2 or name H or \ name HA or name HB2 or name HB3 or name HD21)) or resid 387 through 403 or (res \ id 404 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or r \ esid 405 through 406 or (resid 407 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ2)) or resid 455 through 457)) selection = (chain 'E' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 271 or (resid 272 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) or resid 273 through \ 403 or (resid 404 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 408 through 453 or (resid 454 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE or name NZ or name H or name HA or name HB2 \ or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name \ HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'F' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 225 or (resid 226 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH \ 12)) or resid 227 through 271 or (resid 272 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 th \ rough 403 or (resid 404 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 408 through 453 or (resid 454 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ or name H or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or \ name HE3 or name HZ2)) or resid 455 through 457)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.530 Extract box with map and model: 5.220 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 114.630 Find NCS groups from input model: 1.960 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: 0.020 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.013 0.335 18808 Z= 0.849 Angle : 1.083 14.601 25440 Z= 0.534 Chirality : 0.057 0.328 2693 Planarity : 0.006 0.066 3271 Dihedral : 15.023 179.616 7170 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.15 % Allowed : 7.13 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2190 helix: -0.19 (0.15), residues: 872 sheet: 0.39 (0.28), residues: 333 loop : -0.56 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 424 HIS 0.012 0.003 HIS M 89 PHE 0.036 0.004 PHE E 252 TYR 0.036 0.003 TYR A 238 ARG 0.014 0.001 ARG M 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 510 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 487 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASP cc_start: 0.6970 (m-30) cc_final: 0.6697 (p0) REVERT: B 236 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: B 366 ASN cc_start: 0.7650 (m-40) cc_final: 0.7411 (t0) REVERT: B 370 ASN cc_start: 0.7231 (m-40) cc_final: 0.7023 (m-40) REVERT: C 197 ILE cc_start: 0.9168 (pt) cc_final: 0.8937 (pt) REVERT: C 356 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7359 (mt-10) REVERT: D 321 TYR cc_start: 0.8580 (p90) cc_final: 0.8306 (p90) REVERT: D 419 SER cc_start: 0.8387 (m) cc_final: 0.8089 (t) REVERT: D 422 THR cc_start: 0.7112 (m) cc_final: 0.6806 (t) REVERT: F 200 GLN cc_start: 0.8073 (mt0) cc_final: 0.7491 (mt0) REVERT: F 354 ASP cc_start: 0.8062 (t0) cc_final: 0.7753 (m-30) REVERT: M 48 LYS cc_start: 0.8665 (tttt) cc_final: 0.8396 (tttm) REVERT: M 237 LEU cc_start: 0.8357 (mt) cc_final: 0.8131 (mp) REVERT: N 201 TYR cc_start: 0.8362 (t80) cc_final: 0.8136 (t80) REVERT: N 275 HIS cc_start: 0.6726 (t70) cc_final: 0.6443 (t-90) outliers start: 23 outliers final: 11 residues processed: 507 average time/residue: 0.7663 time to fit residues: 559.5813 Evaluate side-chains 298 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 286 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain M residue 275 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 0.0770 chunk 88 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS B 453 ASN D 285 ASN E 299 HIS ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN M 202 GLN M 284 ASN M 337 GLN N 312 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18808 Z= 0.189 Angle : 0.585 7.200 25440 Z= 0.305 Chirality : 0.040 0.160 2693 Planarity : 0.005 0.048 3271 Dihedral : 10.368 178.838 2591 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.91 % Allowed : 12.35 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2190 helix: 0.92 (0.16), residues: 940 sheet: 0.60 (0.29), residues: 313 loop : -0.34 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 424 HIS 0.006 0.001 HIS N 336 PHE 0.018 0.001 PHE N 265 TYR 0.017 0.001 TYR M 346 ARG 0.006 0.001 ARG M 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 375 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 337 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASP cc_start: 0.6925 (m-30) cc_final: 0.6417 (p0) REVERT: B 236 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: B 370 ASN cc_start: 0.7390 (m-40) cc_final: 0.6932 (m-40) REVERT: C 356 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7369 (mt-10) REVERT: D 189 LYS cc_start: 0.7739 (mttt) cc_final: 0.7527 (mmtm) REVERT: D 419 SER cc_start: 0.8451 (m) cc_final: 0.8143 (t) REVERT: D 448 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7073 (mp10) REVERT: E 271 GLU cc_start: 0.7265 (mp0) cc_final: 0.6943 (pm20) REVERT: E 430 MET cc_start: 0.7445 (mmp) cc_final: 0.6560 (mtm) REVERT: F 327 TYR cc_start: 0.8555 (m-80) cc_final: 0.8302 (m-80) REVERT: F 377 PHE cc_start: 0.6408 (t80) cc_final: 0.6203 (t80) REVERT: F 403 PHE cc_start: 0.7201 (m-80) cc_final: 0.6721 (m-80) REVERT: M 48 LYS cc_start: 0.8737 (tttt) cc_final: 0.8488 (tttm) REVERT: M 82 ILE cc_start: 0.8828 (pt) cc_final: 0.8623 (pt) REVERT: M 201 TYR cc_start: 0.8541 (t80) cc_final: 0.8297 (t80) REVERT: N 267 ARG cc_start: 0.5563 (tpm170) cc_final: 0.1573 (ttp80) REVERT: N 275 HIS cc_start: 0.6796 (t70) cc_final: 0.6327 (t-90) outliers start: 38 outliers final: 26 residues processed: 365 average time/residue: 0.7668 time to fit residues: 414.8510 Evaluate side-chains 298 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 270 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 275 HIS Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 321 ILE Chi-restraints excluded: chain N residue 324 CYS Chi-restraints excluded: chain N residue 342 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN D 285 ASN ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 GLN M 154 ASN ** N 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18808 Z= 0.365 Angle : 0.615 6.188 25440 Z= 0.324 Chirality : 0.041 0.153 2693 Planarity : 0.005 0.056 3271 Dihedral : 10.178 179.169 2584 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.56 % Allowed : 13.86 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2190 helix: 0.86 (0.16), residues: 946 sheet: 0.13 (0.27), residues: 344 loop : -0.47 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 424 HIS 0.010 0.001 HIS M 89 PHE 0.018 0.002 PHE M 208 TYR 0.023 0.002 TYR B 440 ARG 0.005 0.001 ARG M 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 282 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 189 LYS cc_start: 0.7932 (mttt) cc_final: 0.7605 (mmtm) REVERT: D 379 GLU cc_start: 0.7442 (tt0) cc_final: 0.6984 (tp30) REVERT: D 419 SER cc_start: 0.8560 (m) cc_final: 0.8247 (t) REVERT: E 271 GLU cc_start: 0.7498 (mp0) cc_final: 0.7084 (pm20) REVERT: E 415 GLU cc_start: 0.6677 (tp30) cc_final: 0.5362 (pt0) REVERT: E 430 MET cc_start: 0.7415 (mmp) cc_final: 0.6751 (mtm) REVERT: F 374 GLU cc_start: 0.6854 (pt0) cc_final: 0.6549 (tt0) REVERT: F 423 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7314 (tp40) REVERT: M 48 LYS cc_start: 0.8877 (tttt) cc_final: 0.8509 (tttm) REVERT: N 204 PHE cc_start: 0.7693 (t80) cc_final: 0.6753 (m-80) REVERT: N 275 HIS cc_start: 0.6957 (t70) cc_final: 0.6511 (t-90) REVERT: N 281 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7712 (mp10) outliers start: 51 outliers final: 39 residues processed: 324 average time/residue: 0.7401 time to fit residues: 362.2218 Evaluate side-chains 297 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 366 ASN Chi-restraints excluded: chain E residue 383 GLN Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 424 TRP Chi-restraints excluded: chain M residue 97 ASP Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 275 HIS Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 281 GLN Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 324 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18808 Z= 0.303 Angle : 0.561 6.548 25440 Z= 0.293 Chirality : 0.040 0.149 2693 Planarity : 0.004 0.046 3271 Dihedral : 9.691 178.757 2578 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.91 % Allowed : 14.11 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2190 helix: 0.82 (0.17), residues: 955 sheet: -0.00 (0.28), residues: 314 loop : -0.57 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 287 HIS 0.008 0.001 HIS M 89 PHE 0.018 0.001 PHE M 208 TYR 0.014 0.001 TYR E 238 ARG 0.007 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 286 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 VAL cc_start: 0.9039 (t) cc_final: 0.8753 (p) REVERT: C 292 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7416 (mm-30) REVERT: D 189 LYS cc_start: 0.8042 (mttt) cc_final: 0.7660 (mmtm) REVERT: D 379 GLU cc_start: 0.7498 (tt0) cc_final: 0.6987 (tp30) REVERT: D 419 SER cc_start: 0.8647 (m) cc_final: 0.8259 (t) REVERT: D 448 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: E 271 GLU cc_start: 0.7536 (mp0) cc_final: 0.7123 (pm20) REVERT: E 415 GLU cc_start: 0.6810 (tp30) cc_final: 0.5312 (pt0) REVERT: F 310 LEU cc_start: 0.8598 (mt) cc_final: 0.8292 (mt) REVERT: F 327 TYR cc_start: 0.8574 (m-80) cc_final: 0.8249 (m-80) REVERT: F 374 GLU cc_start: 0.7062 (pt0) cc_final: 0.6680 (tt0) REVERT: M 48 LYS cc_start: 0.8844 (tttt) cc_final: 0.8572 (tttm) REVERT: N 204 PHE cc_start: 0.7656 (t80) cc_final: 0.6740 (m-80) REVERT: N 275 HIS cc_start: 0.7013 (t70) cc_final: 0.6588 (t-90) outliers start: 58 outliers final: 46 residues processed: 330 average time/residue: 0.7153 time to fit residues: 359.9454 Evaluate side-chains 309 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 262 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 366 ASN Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 424 TRP Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain M residue 97 ASP Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 275 HIS Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 324 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18808 Z= 0.202 Angle : 0.509 6.227 25440 Z= 0.262 Chirality : 0.039 0.148 2693 Planarity : 0.004 0.057 3271 Dihedral : 9.249 179.512 2578 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.51 % Allowed : 15.41 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2190 helix: 1.09 (0.17), residues: 952 sheet: -0.05 (0.28), residues: 334 loop : -0.46 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 424 HIS 0.005 0.001 HIS M 89 PHE 0.015 0.001 PHE M 208 TYR 0.012 0.001 TYR M 346 ARG 0.003 0.000 ARG M 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 290 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 VAL cc_start: 0.9047 (t) cc_final: 0.8792 (p) REVERT: D 189 LYS cc_start: 0.8113 (mttt) cc_final: 0.7741 (mmtm) REVERT: D 379 GLU cc_start: 0.7481 (tt0) cc_final: 0.7274 (tm-30) REVERT: D 419 SER cc_start: 0.8507 (m) cc_final: 0.8169 (t) REVERT: E 271 GLU cc_start: 0.7547 (mp0) cc_final: 0.7074 (pm20) REVERT: E 415 GLU cc_start: 0.6714 (tp30) cc_final: 0.5162 (pt0) REVERT: E 430 MET cc_start: 0.7321 (mmp) cc_final: 0.6582 (mtm) REVERT: F 327 TYR cc_start: 0.8512 (m-80) cc_final: 0.8182 (m-80) REVERT: F 370 ASN cc_start: 0.8252 (m-40) cc_final: 0.7393 (t0) REVERT: F 374 GLU cc_start: 0.6913 (pt0) cc_final: 0.6590 (tt0) REVERT: M 37 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6637 (p0) REVERT: M 48 LYS cc_start: 0.8772 (tttt) cc_final: 0.8483 (tttm) REVERT: N 204 PHE cc_start: 0.7525 (t80) cc_final: 0.6687 (m-80) REVERT: N 275 HIS cc_start: 0.6987 (t70) cc_final: 0.6496 (t-90) REVERT: N 348 LYS cc_start: 0.5353 (mttt) cc_final: 0.4413 (pttm) outliers start: 50 outliers final: 39 residues processed: 328 average time/residue: 0.7414 time to fit residues: 367.9295 Evaluate side-chains 307 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 267 time to evaluate : 2.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 366 ASN Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 424 TRP Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 275 HIS Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 324 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 211 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18808 Z= 0.209 Angle : 0.507 5.653 25440 Z= 0.260 Chirality : 0.039 0.155 2693 Planarity : 0.004 0.051 3271 Dihedral : 9.132 179.302 2578 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.61 % Allowed : 15.96 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2190 helix: 1.23 (0.17), residues: 956 sheet: -0.04 (0.28), residues: 329 loop : -0.54 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 424 HIS 0.006 0.001 HIS M 89 PHE 0.015 0.001 PHE D 178 TYR 0.012 0.001 TYR E 238 ARG 0.005 0.000 ARG N 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 285 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8470 (ttpm) REVERT: C 292 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7318 (mm-30) REVERT: D 189 LYS cc_start: 0.8232 (mttt) cc_final: 0.7744 (mmtm) REVERT: D 419 SER cc_start: 0.8540 (m) cc_final: 0.8182 (t) REVERT: E 271 GLU cc_start: 0.7555 (mp0) cc_final: 0.7078 (pm20) REVERT: E 415 GLU cc_start: 0.6593 (tp30) cc_final: 0.5094 (pt0) REVERT: E 430 MET cc_start: 0.7300 (mmp) cc_final: 0.6643 (ptm) REVERT: F 327 TYR cc_start: 0.8507 (m-80) cc_final: 0.8162 (m-80) REVERT: F 370 ASN cc_start: 0.8308 (m-40) cc_final: 0.7390 (t0) REVERT: M 37 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6513 (p0) REVERT: M 233 GLN cc_start: 0.7107 (mm110) cc_final: 0.6620 (mm-40) REVERT: N 204 PHE cc_start: 0.7489 (t80) cc_final: 0.6649 (m-80) REVERT: N 222 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6717 (m-10) REVERT: N 275 HIS cc_start: 0.7061 (t70) cc_final: 0.6569 (t-90) REVERT: N 281 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7622 (mp10) outliers start: 52 outliers final: 43 residues processed: 322 average time/residue: 0.6952 time to fit residues: 338.2082 Evaluate side-chains 310 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 263 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 366 ASN Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 287 TRP Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 222 TYR Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 281 GLN Chi-restraints excluded: chain N residue 324 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 120 optimal weight: 0.0970 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN B 370 ASN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18808 Z= 0.205 Angle : 0.502 6.515 25440 Z= 0.257 Chirality : 0.039 0.149 2693 Planarity : 0.004 0.051 3271 Dihedral : 9.011 179.501 2576 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.71 % Allowed : 16.32 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2190 helix: 1.29 (0.17), residues: 960 sheet: -0.08 (0.28), residues: 327 loop : -0.59 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 424 HIS 0.005 0.001 HIS M 89 PHE 0.014 0.001 PHE M 208 TYR 0.014 0.001 TYR B 344 ARG 0.007 0.000 ARG N 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 273 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: B 236 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: D 189 LYS cc_start: 0.8327 (mttt) cc_final: 0.7776 (mmtm) REVERT: D 269 GLN cc_start: 0.7040 (mp10) cc_final: 0.6618 (mp10) REVERT: D 419 SER cc_start: 0.8550 (m) cc_final: 0.8198 (t) REVERT: E 271 GLU cc_start: 0.7496 (mp0) cc_final: 0.7023 (pm20) REVERT: E 415 GLU cc_start: 0.6576 (tp30) cc_final: 0.5115 (pt0) REVERT: E 430 MET cc_start: 0.7327 (mmp) cc_final: 0.6701 (ptt) REVERT: F 370 ASN cc_start: 0.8289 (m-40) cc_final: 0.7401 (t0) REVERT: M 37 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.6484 (p0) REVERT: N 204 PHE cc_start: 0.7384 (t80) cc_final: 0.6531 (m-80) REVERT: N 222 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6709 (m-10) REVERT: N 275 HIS cc_start: 0.7032 (t70) cc_final: 0.6514 (t-90) REVERT: N 281 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7631 (mp10) outliers start: 54 outliers final: 45 residues processed: 312 average time/residue: 0.6907 time to fit residues: 323.8689 Evaluate side-chains 315 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 265 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 366 ASN Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 424 TRP Chi-restraints excluded: chain M residue 37 ASN Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 287 TRP Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 222 TYR Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 281 GLN Chi-restraints excluded: chain N residue 324 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18808 Z= 0.176 Angle : 0.491 6.340 25440 Z= 0.249 Chirality : 0.038 0.153 2693 Planarity : 0.004 0.052 3271 Dihedral : 8.890 179.504 2576 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.31 % Allowed : 16.92 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2190 helix: 1.45 (0.17), residues: 960 sheet: -0.02 (0.29), residues: 327 loop : -0.57 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 424 HIS 0.005 0.001 HIS A 407 PHE 0.015 0.001 PHE D 178 TYR 0.011 0.001 TYR A 446 ARG 0.006 0.000 ARG N 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 328 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 282 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: B 236 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: D 189 LYS cc_start: 0.8390 (mttt) cc_final: 0.7842 (mmtm) REVERT: D 269 GLN cc_start: 0.6978 (mp10) cc_final: 0.6576 (mp10) REVERT: D 379 GLU cc_start: 0.7421 (tt0) cc_final: 0.7066 (tm-30) REVERT: D 419 SER cc_start: 0.8558 (m) cc_final: 0.8208 (t) REVERT: E 271 GLU cc_start: 0.7517 (mp0) cc_final: 0.7044 (pm20) REVERT: E 415 GLU cc_start: 0.6554 (tp30) cc_final: 0.5159 (pt0) REVERT: E 430 MET cc_start: 0.7325 (mmp) cc_final: 0.6639 (ptm) REVERT: F 370 ASN cc_start: 0.8240 (m-40) cc_final: 0.7366 (t0) REVERT: N 204 PHE cc_start: 0.7378 (t80) cc_final: 0.6454 (m-80) REVERT: N 222 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6697 (m-10) REVERT: N 275 HIS cc_start: 0.7056 (t70) cc_final: 0.6550 (t-90) REVERT: N 281 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7629 (mp10) outliers start: 46 outliers final: 37 residues processed: 314 average time/residue: 0.7120 time to fit residues: 339.2554 Evaluate side-chains 306 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 265 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 366 ASN Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 424 TRP Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 287 TRP Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 222 TYR Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 281 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 196 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18808 Z= 0.195 Angle : 0.499 6.036 25440 Z= 0.253 Chirality : 0.038 0.148 2693 Planarity : 0.004 0.052 3271 Dihedral : 8.888 179.564 2576 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.51 % Allowed : 16.77 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2190 helix: 1.49 (0.17), residues: 960 sheet: -0.02 (0.28), residues: 327 loop : -0.57 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 424 HIS 0.005 0.001 HIS M 89 PHE 0.014 0.001 PHE M 208 TYR 0.012 0.001 TYR B 344 ARG 0.007 0.000 ARG N 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 274 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: B 236 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: D 189 LYS cc_start: 0.8390 (mttt) cc_final: 0.7788 (mmtm) REVERT: D 269 GLN cc_start: 0.7005 (mp10) cc_final: 0.6663 (mp10) REVERT: D 379 GLU cc_start: 0.7431 (tt0) cc_final: 0.7080 (tm-30) REVERT: D 419 SER cc_start: 0.8573 (m) cc_final: 0.8218 (t) REVERT: E 271 GLU cc_start: 0.7543 (mp0) cc_final: 0.7069 (pm20) REVERT: E 415 GLU cc_start: 0.6545 (tp30) cc_final: 0.5152 (pt0) REVERT: E 430 MET cc_start: 0.7327 (mmp) cc_final: 0.6549 (mtm) REVERT: F 370 ASN cc_start: 0.8238 (m-40) cc_final: 0.7375 (t0) REVERT: N 204 PHE cc_start: 0.7380 (t80) cc_final: 0.6451 (m-80) REVERT: N 222 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: N 275 HIS cc_start: 0.7046 (t70) cc_final: 0.6523 (t-90) REVERT: N 281 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7634 (mp10) outliers start: 50 outliers final: 40 residues processed: 311 average time/residue: 0.6855 time to fit residues: 322.8200 Evaluate side-chains 313 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 269 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 366 ASN Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 424 TRP Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 287 TRP Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 222 TYR Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 281 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18808 Z= 0.358 Angle : 0.577 6.053 25440 Z= 0.301 Chirality : 0.041 0.150 2693 Planarity : 0.005 0.057 3271 Dihedral : 9.336 179.605 2576 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.56 % Allowed : 16.87 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2190 helix: 1.09 (0.17), residues: 958 sheet: -0.35 (0.28), residues: 322 loop : -0.73 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 451 HIS 0.010 0.001 HIS M 89 PHE 0.019 0.002 PHE M 208 TYR 0.016 0.002 TYR E 238 ARG 0.007 0.001 ARG N 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 260 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7669 (mt0) REVERT: B 236 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: D 189 LYS cc_start: 0.8414 (mttt) cc_final: 0.7811 (mmtm) REVERT: D 379 GLU cc_start: 0.7550 (tt0) cc_final: 0.7171 (tm-30) REVERT: D 419 SER cc_start: 0.8648 (m) cc_final: 0.8266 (t) REVERT: E 271 GLU cc_start: 0.7553 (mp0) cc_final: 0.7072 (pm20) REVERT: E 415 GLU cc_start: 0.6760 (tp30) cc_final: 0.5301 (pt0) REVERT: F 370 ASN cc_start: 0.8226 (m-40) cc_final: 0.7456 (t0) REVERT: N 199 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8484 (tt) REVERT: N 204 PHE cc_start: 0.7535 (t80) cc_final: 0.6640 (m-80) REVERT: N 222 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6503 (m-10) REVERT: N 275 HIS cc_start: 0.7089 (t70) cc_final: 0.6689 (t-90) REVERT: N 281 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7609 (mp10) outliers start: 51 outliers final: 44 residues processed: 301 average time/residue: 0.7281 time to fit residues: 330.9829 Evaluate side-chains 302 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 253 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 366 ASN Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 424 TRP Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 250 SER Chi-restraints excluded: chain M residue 287 TRP Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 222 TYR Chi-restraints excluded: chain N residue 241 MET Chi-restraints excluded: chain N residue 281 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114638 restraints weight = 74800.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119446 restraints weight = 34272.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122465 restraints weight = 20958.129| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18808 Z= 0.187 Angle : 0.507 6.532 25440 Z= 0.258 Chirality : 0.039 0.150 2693 Planarity : 0.004 0.066 3271 Dihedral : 9.018 179.567 2576 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.11 % Allowed : 17.72 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2190 helix: 1.41 (0.17), residues: 946 sheet: -0.20 (0.28), residues: 323 loop : -0.70 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 424 HIS 0.004 0.001 HIS M 89 PHE 0.014 0.001 PHE D 442 TYR 0.016 0.001 TYR N 201 ARG 0.011 0.000 ARG D 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7864.71 seconds wall clock time: 139 minutes 23.10 seconds (8363.10 seconds total)