Starting phenix.real_space_refine (version: dev) on Mon Dec 19 18:33:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/12_2022/6hz4_0310_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/12_2022/6hz4_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_0310/12_2022/6hz4_0310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/12_2022/6hz4_0310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/12_2022/6hz4_0310_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz4_0310/12_2022/6hz4_0310_trim.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Convert atoms to be neutral 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 17.02, per 1000 atoms: 0.47 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: 30.76 Conformation dependent library (CDL) restraints added in 3.1 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: 0.94 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: 13.17 Time building geometry restraints manager: 31.52 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: 14542 35.92 - 71.85: 269 71.85 - 107.77: 13 107.77 - 143.69: 1 143.69 - 179.62: 6 Dihedral angle restraints: 14831 sinusoidal: 6960 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 14828 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 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. 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: 0.700 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.780 Extract box with map and model: 6.300 Check model and map are aligned: 0.550 Convert atoms to be neutral: 0.340 Process input model: 109.620 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 14.994 179.616 7086 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.15 % 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 *********************** 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 : 3.019 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 outliers start: 23 outliers final: 11 residues processed: 507 average time/residue: 0.7153 time to fit residues: 530.7190 Evaluate side-chains 294 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 283 time to evaluate : 2.941 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.4287 time to fit residues: 11.9455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 56 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 18808 Z= 0.194 Angle : 0.593 6.989 25440 Z= 0.310 Chirality : 0.040 0.159 2693 Planarity : 0.005 0.046 3271 Dihedral : 9.755 178.017 2483 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2190 helix: 0.89 (0.16), residues: 940 sheet: 0.57 (0.29), residues: 309 loop : -0.38 (0.19), residues: 941 *********************** 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 362 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 332 time to evaluate : 3.004 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 outliers start: 30 outliers final: 21 residues processed: 356 average time/residue: 0.6976 time to fit residues: 373.6950 Evaluate side-chains 287 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 266 time to evaluate : 2.946 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.3964 time to fit residues: 19.2155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 285 ASN ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 GLN M 154 ASN ** N 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 18808 Z= 0.289 Angle : 0.577 5.880 25440 Z= 0.301 Chirality : 0.040 0.153 2693 Planarity : 0.004 0.053 3271 Dihedral : 9.458 179.163 2483 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2190 helix: 0.95 (0.16), residues: 948 sheet: 0.31 (0.29), residues: 315 loop : -0.45 (0.19), residues: 927 *********************** 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 316 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 291 time to evaluate : 2.827 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 outliers start: 25 outliers final: 18 residues processed: 308 average time/residue: 0.6995 time to fit residues: 324.3164 Evaluate side-chains 280 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 3.464 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.4333 time to fit residues: 17.9935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 22 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 18808 Z= 0.473 Angle : 0.662 7.786 25440 Z= 0.352 Chirality : 0.044 0.158 2693 Planarity : 0.005 0.043 3271 Dihedral : 9.557 179.105 2483 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2190 helix: 0.49 (0.16), residues: 947 sheet: -0.43 (0.27), residues: 336 loop : -0.71 (0.20), residues: 907 *********************** 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 320 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 282 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 308 average time/residue: 0.6697 time to fit residues: 315.9766 Evaluate side-chains 280 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 256 time to evaluate : 2.838 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.4281 time to fit residues: 22.2943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** 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: 0.7889 moved from start: 0.4728 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= 0.178 Angle : 0.518 6.692 25440 Z= 0.265 Chirality : 0.039 0.148 2693 Planarity : 0.004 0.056 3271 Dihedral : 8.919 179.708 2483 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.80 % 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: 0.14 (0.18), residues: 2190 helix: 0.97 (0.17), residues: 943 sheet: -0.19 (0.29), residues: 312 loop : -0.63 (0.19), residues: 935 *********************** 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 304 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 288 time to evaluate : 2.931 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 outliers start: 16 outliers final: 10 residues processed: 298 average time/residue: 0.6650 time to fit residues: 300.5593 Evaluate side-chains 268 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 2.987 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.4443 time to fit residues: 11.7193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.0980 chunk 211 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 GLN ** 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: 0.7867 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18808 Z= 0.159 Angle : 0.495 5.671 25440 Z= 0.251 Chirality : 0.038 0.154 2693 Planarity : 0.004 0.054 3271 Dihedral : 8.644 179.657 2483 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.90 % 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 (0.18), residues: 2190 helix: 1.30 (0.17), residues: 951 sheet: 0.02 (0.29), residues: 306 loop : -0.51 (0.20), residues: 933 *********************** 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 305 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 287 time to evaluate : 2.951 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 outliers start: 18 outliers final: 10 residues processed: 297 average time/residue: 0.6848 time to fit residues: 306.7775 Evaluate side-chains 269 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 259 time to evaluate : 2.726 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.4621 time to fit residues: 11.8031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 120 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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** ** F 200 GLN ** 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: 0.7897 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 18808 Z= 0.235 Angle : 0.520 7.260 25440 Z= 0.265 Chirality : 0.039 0.143 2693 Planarity : 0.004 0.051 3271 Dihedral : 8.676 179.362 2483 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2190 helix: 1.26 (0.17), residues: 953 sheet: -0.19 (0.28), residues: 322 loop : -0.55 (0.20), residues: 915 *********************** 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 287 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 276 time to evaluate : 3.256 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 outliers start: 11 outliers final: 7 residues processed: 283 average time/residue: 0.7000 time to fit residues: 303.1305 Evaluate side-chains 260 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 253 time to evaluate : 3.054 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.4505 time to fit residues: 9.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 165 optimal weight: 2.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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** ** F 200 GLN ** 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: 0.7870 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 18808 Z= 0.167 Angle : 0.495 6.995 25440 Z= 0.250 Chirality : 0.038 0.152 2693 Planarity : 0.004 0.050 3271 Dihedral : 8.516 179.708 2483 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.65 % 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: 1.53 (0.17), residues: 943 sheet: 0.02 (0.30), residues: 299 loop : -0.60 (0.19), residues: 948 *********************** 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 289 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 276 time to evaluate : 3.082 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 outliers start: 13 outliers final: 8 residues processed: 285 average time/residue: 0.6671 time to fit residues: 288.7158 Evaluate side-chains 272 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 2.659 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.5147 time to fit residues: 10.3239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 154 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 ASN ** F 200 GLN ** 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: 0.7867 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 18808 Z= 0.172 Angle : 0.500 7.902 25440 Z= 0.251 Chirality : 0.038 0.153 2693 Planarity : 0.004 0.052 3271 Dihedral : 8.453 179.721 2483 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2190 helix: 1.63 (0.17), residues: 943 sheet: -0.03 (0.29), residues: 319 loop : -0.53 (0.20), residues: 928 *********************** 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 279 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 269 time to evaluate : 2.896 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 outliers start: 10 outliers final: 7 residues processed: 277 average time/residue: 0.7000 time to fit residues: 295.3392 Evaluate side-chains 271 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 264 time to evaluate : 3.058 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.5342 time to fit residues: 10.0498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 0.0470 chunk 126 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 173 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 ASN ** F 200 GLN ** 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: 0.7890 moved from start: 0.5412 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= 0.228 Angle : 0.521 8.799 25440 Z= 0.264 Chirality : 0.039 0.148 2693 Planarity : 0.004 0.054 3271 Dihedral : 8.506 179.664 2483 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.20 % 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: 0.63 (0.18), residues: 2190 helix: 1.60 (0.17), residues: 941 sheet: -0.14 (0.28), residues: 319 loop : -0.56 (0.19), residues: 930 ********************** 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 268 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 267 average time/residue: 0.6922 time to fit residues: 280.9199 Evaluate side-chains 261 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 257 time to evaluate : 3.172 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.4866 time to fit residues: 7.2083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 0.1980 chunk 25 optimal weight: 0.0770 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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** C 426 ASN ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118060 restraints weight = 74069.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123081 restraints weight = 33864.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126188 restraints weight = 20617.494| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 18808 Z= 0.143 Angle : 0.496 8.932 25440 Z= 0.247 Chirality : 0.038 0.153 2693 Planarity : 0.004 0.054 3271 Dihedral : 8.303 179.631 2483 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.30 % 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: 0.80 (0.18), residues: 2190 helix: 1.77 (0.17), residues: 953 sheet: -0.02 (0.29), residues: 319 loop : -0.54 (0.19), residues: 918 =============================================================================== Job complete usr+sys time: 7235.40 seconds wall clock time: 128 minutes 20.02 seconds (7700.02 seconds total)