Starting phenix.real_space_refine on Fri Jul 26 09:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/07_2024/6pp8_20422_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/07_2024/6pp8_20422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/07_2024/6pp8_20422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/07_2024/6pp8_20422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/07_2024/6pp8_20422_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/07_2024/6pp8_20422_trim.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 S 35 5.16 5 C 10120 2.51 5 N 2720 2.21 5 O 3209 1.98 5 H 16234 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 392": "OD1" <-> "OD2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C ASP 392": "OD1" <-> "OD2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D ASP 347": "OD1" <-> "OD2" Residue "D ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 392": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32335 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5273 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 2 Chain: "B" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5409 Classifications: {'peptide': 351} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain breaks: 1 Chain: "C" Number of atoms: 5396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5396 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "D" Number of atoms: 5377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5377 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "E" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5395 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 2 Chain: "F" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5244 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 59 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.75, per 1000 atoms: 0.43 Number of scatterers: 32335 At special positions: 0 Unit cell: (146.16, 140.36, 102.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 17 15.00 O 3209 8.00 N 2720 7.00 C 10120 6.00 H 16234 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.67 Conformation dependent library (CDL) restraints added in 3.1 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 53.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.706A pdb=" N ASP A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 102 removed outlier: 3.790A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 99 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 Processing helix chain 'A' and resid 158 through 170 removed outlier: 4.101A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.540A pdb=" N ILE A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.642A pdb=" N GLN A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.583A pdb=" N GLY A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 removed outlier: 4.066A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.891A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 299' Processing helix chain 'A' and resid 301 through 307 removed outlier: 3.514A pdb=" N ARG A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.679A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.547A pdb=" N LEU A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.815A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.580A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.915A pdb=" N ILE A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.791A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 removed outlier: 3.565A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.692A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.506A pdb=" N LEU B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.577A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.597A pdb=" N ASP B 194 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN B 195 " --> pdb=" O LYS B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 195' Processing helix chain 'B' and resid 204 through 215 removed outlier: 3.926A pdb=" N GLN B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.707A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.737A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.598A pdb=" N ARG B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.570A pdb=" N ILE B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.838A pdb=" N LEU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.735A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.779A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.726A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 3.809A pdb=" N LYS C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.542A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 170 removed outlier: 4.161A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.508A pdb=" N LYS C 188 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.904A pdb=" N GLN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.829A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.868A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.673A pdb=" N LEU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 removed outlier: 3.770A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.648A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.717A pdb=" N LEU C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.006A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.638A pdb=" N ALA C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.844A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.706A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.906A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.618A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.543A pdb=" N LYS D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 186 through 190 Processing helix chain 'D' and resid 204 through 215 removed outlier: 3.877A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.927A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 264 " --> pdb=" O HIS D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 removed outlier: 3.716A pdb=" N ALA D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.605A pdb=" N LEU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.753A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.691A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 removed outlier: 3.675A pdb=" N LEU D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 removed outlier: 3.529A pdb=" N LEU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 371 Processing helix chain 'D' and resid 372 through 380 removed outlier: 3.742A pdb=" N ALA D 379 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.661A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 76 removed outlier: 3.674A pdb=" N ASP E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 101 Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.524A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 204 through 217 removed outlier: 3.553A pdb=" N GLN E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.553A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.652A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.554A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 307 Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.783A pdb=" N ILE E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 343 removed outlier: 3.685A pdb=" N LEU E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 removed outlier: 4.085A pdb=" N ALA E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 371 Processing helix chain 'E' and resid 372 through 380 removed outlier: 3.601A pdb=" N VAL E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 379 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 399 through 405 removed outlier: 3.867A pdb=" N ILE E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.577A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 102 removed outlier: 3.578A pdb=" N LYS F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.640A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 removed outlier: 4.126A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 204 through 217 removed outlier: 4.199A pdb=" N GLN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 211 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 227 removed outlier: 3.607A pdb=" N GLY F 227 " --> pdb=" O PRO F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 262 removed outlier: 4.072A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 removed outlier: 3.989A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.635A pdb=" N LEU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.761A pdb=" N ARG F 307 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'F' and resid 332 through 345 removed outlier: 4.031A pdb=" N LEU F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 removed outlier: 3.588A pdb=" N LEU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP F 356 " --> pdb=" O ASP F 352 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 380 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 399 through 405 removed outlier: 3.547A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 removed outlier: 3.831A pdb=" N THR A 141 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 182 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 115 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.917A pdb=" N ASP A 347 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 144 removed outlier: 3.630A pdb=" N ASP B 184 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.864A pdb=" N ALA B 220 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 222 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 236 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.760A pdb=" N ILE B 398 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 144 removed outlier: 3.672A pdb=" N THR C 141 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 182 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 349 through 350 removed outlier: 4.019A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 143 through 144 removed outlier: 3.714A pdb=" N ASP D 184 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.062A pdb=" N LYS D 395 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 144 removed outlier: 3.633A pdb=" N ALA E 143 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP E 184 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU E 116 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.943A pdb=" N ALA E 220 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 238 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 347 through 348 removed outlier: 6.872A pdb=" N ASP E 347 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 140 through 144 removed outlier: 3.745A pdb=" N THR F 141 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL F 181 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 219 through 222 removed outlier: 3.859A pdb=" N ALA F 220 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL F 238 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 395 through 397 removed outlier: 3.513A pdb=" N LYS F 395 " --> pdb=" O ILE F 412 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1671 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: 11.50 Time building geometry restraints manager: 24.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 16228 1.05 - 1.27: 2877 1.27 - 1.50: 6185 1.50 - 1.72: 7192 1.72 - 1.95: 59 Bond restraints: 32541 Sorted by residual: bond pdb=" N SER B 62 " pdb=" H1 SER B 62 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N GLU D 234 " pdb=" CA GLU D 234 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.29e-02 6.01e+03 7.54e+00 bond pdb=" N PHE D 235 " pdb=" H PHE D 235 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C VAL C 238 " pdb=" N ASP C 239 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.29e-02 6.01e+03 6.58e+00 bond pdb=" N LEU D 236 " pdb=" CA LEU D 236 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.53e+00 ... (remaining 32536 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.54: 2358 107.54 - 114.70: 40496 114.70 - 121.85: 10650 121.85 - 129.01: 5584 129.01 - 136.17: 86 Bond angle restraints: 59174 Sorted by residual: angle pdb=" N ALA F 151 " pdb=" CA ALA F 151 " pdb=" C ALA F 151 " ideal model delta sigma weight residual 111.24 119.64 -8.40 1.38e+00 5.25e-01 3.71e+01 angle pdb=" N SER E 266 " pdb=" CA SER E 266 " pdb=" C SER E 266 " ideal model delta sigma weight residual 109.72 115.67 -5.95 1.60e+00 3.91e-01 1.38e+01 angle pdb=" N GLY F 265 " pdb=" CA GLY F 265 " pdb=" C GLY F 265 " ideal model delta sigma weight residual 113.18 104.69 8.49 2.37e+00 1.78e-01 1.28e+01 angle pdb=" CA GLN D 233 " pdb=" C GLN D 233 " pdb=" O GLN D 233 " ideal model delta sigma weight residual 121.84 117.87 3.97 1.16e+00 7.43e-01 1.17e+01 angle pdb=" O VAL C 238 " pdb=" C VAL C 238 " pdb=" N ASP C 239 " ideal model delta sigma weight residual 122.97 119.89 3.08 9.00e-01 1.23e+00 1.17e+01 ... (remaining 59169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13561 17.86 - 35.71: 1133 35.71 - 53.57: 307 53.57 - 71.43: 69 71.43 - 89.28: 8 Dihedral angle restraints: 15078 sinusoidal: 8574 harmonic: 6504 Sorted by residual: dihedral pdb=" CD ARG D 307 " pdb=" NE ARG D 307 " pdb=" CZ ARG D 307 " pdb=" NH1 ARG D 307 " ideal model delta sinusoidal sigma weight residual 0.00 32.18 -32.18 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CA ASP E 137 " pdb=" CB ASP E 137 " pdb=" CG ASP E 137 " pdb=" OD1 ASP E 137 " ideal model delta sinusoidal sigma weight residual -30.00 -83.64 53.64 1 2.00e+01 2.50e-03 9.77e+00 dihedral pdb=" CB GLU D 285 " pdb=" CG GLU D 285 " pdb=" CD GLU D 285 " pdb=" OE1 GLU D 285 " ideal model delta sinusoidal sigma weight residual 0.00 84.76 -84.76 1 3.00e+01 1.11e-03 9.69e+00 ... (remaining 15075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1751 0.034 - 0.067: 542 0.067 - 0.101: 191 0.101 - 0.134: 111 0.134 - 0.168: 14 Chirality restraints: 2609 Sorted by residual: chirality pdb=" CA LEU D 236 " pdb=" N LEU D 236 " pdb=" C LEU D 236 " pdb=" CB LEU D 236 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA ILE F 301 " pdb=" N ILE F 301 " pdb=" C ILE F 301 " pdb=" CB ILE F 301 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ILE E 301 " pdb=" N ILE E 301 " pdb=" C ILE E 301 " pdb=" CB ILE E 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 2606 not shown) Planarity restraints: 4828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 307 " 0.600 9.50e-02 1.11e+02 2.00e-01 4.23e+01 pdb=" NE ARG D 307 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 307 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 307 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 307 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG D 307 " -0.010 2.00e-02 2.50e+03 pdb="HH12 ARG D 307 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG D 307 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG D 307 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 123 " -0.029 2.00e-02 2.50e+03 5.86e-02 3.43e+01 pdb=" C SER E 123 " 0.101 2.00e-02 2.50e+03 pdb=" O SER E 123 " -0.038 2.00e-02 2.50e+03 pdb=" N GLY E 124 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " -0.325 9.50e-02 1.11e+02 1.08e-01 1.24e+01 pdb=" NE ARG A 98 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " -0.007 2.00e-02 2.50e+03 ... (remaining 4825 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 151 2.02 - 2.67: 47795 2.67 - 3.31: 90896 3.31 - 3.96: 111576 3.96 - 4.60: 177381 Nonbonded interactions: 427799 Sorted by model distance: nonbonded pdb=" HH TYR F 96 " pdb=" O ARG F 178 " model vdw 1.379 1.850 nonbonded pdb=" O GLU B 263 " pdb=" HG1 THR B 264 " model vdw 1.450 1.850 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.463 1.850 nonbonded pdb=" HZ3 LYS F 125 " pdb=" O1B ADP F 600 " model vdw 1.493 1.850 nonbonded pdb=" O LEU B 326 " pdb=" HG1 THR B 334 " model vdw 1.540 1.850 ... (remaining 427794 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 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'B' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'C' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'D' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'E' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'F' and (resid 65 through 192 or resid 201 through 227 or resid 233 throu \ gh 259 or (resid 260 and (name N or name CA or name C or name O or name CB or na \ me CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or na \ me HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 261 through 41 \ 3)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.470 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 93.420 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.003 0.035 16307 Z= 0.223 Angle : 0.720 9.280 22075 Z= 0.400 Chirality : 0.043 0.168 2609 Planarity : 0.007 0.258 2840 Dihedral : 12.437 89.282 6194 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.16), residues: 2047 helix: -1.87 (0.15), residues: 728 sheet: -1.64 (0.27), residues: 272 loop : -1.20 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 95 PHE 0.008 0.001 PHE A 140 TYR 0.017 0.001 TYR F 96 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7940 (t80) cc_final: 0.7626 (t80) REVERT: A 245 PHE cc_start: 0.5181 (m-80) cc_final: 0.4942 (m-80) REVERT: A 287 LEU cc_start: 0.8856 (mt) cc_final: 0.8632 (mp) REVERT: A 317 LEU cc_start: 0.7186 (mt) cc_final: 0.6919 (mt) REVERT: B 279 ASP cc_start: 0.8742 (m-30) cc_final: 0.8401 (t0) REVERT: B 293 GLU cc_start: 0.9011 (tt0) cc_final: 0.8383 (tm-30) REVERT: B 393 VAL cc_start: 0.8875 (t) cc_final: 0.8643 (m) REVERT: C 136 LEU cc_start: 0.8758 (tp) cc_final: 0.8480 (tp) REVERT: C 243 ILE cc_start: 0.8638 (mt) cc_final: 0.8078 (tp) REVERT: C 294 ASP cc_start: 0.8891 (m-30) cc_final: 0.8656 (m-30) REVERT: C 319 GLU cc_start: 0.8956 (pt0) cc_final: 0.8724 (pm20) REVERT: C 352 ASP cc_start: 0.8824 (p0) cc_final: 0.8321 (t0) REVERT: C 366 LYS cc_start: 0.9439 (mmtt) cc_final: 0.9237 (mmmt) REVERT: D 130 GLU cc_start: 0.9107 (tt0) cc_final: 0.8331 (tm-30) REVERT: D 182 TYR cc_start: 0.8926 (t80) cc_final: 0.8323 (t80) REVERT: D 201 ASP cc_start: 0.8918 (m-30) cc_final: 0.8410 (p0) REVERT: D 256 LYS cc_start: 0.8699 (mttt) cc_final: 0.8424 (mmmt) REVERT: D 285 GLU cc_start: 0.8643 (tp30) cc_final: 0.8402 (tp30) REVERT: E 69 GLU cc_start: 0.9252 (tt0) cc_final: 0.8997 (mt-10) REVERT: E 144 ASP cc_start: 0.7931 (t0) cc_final: 0.6479 (t0) REVERT: E 170 ASP cc_start: 0.8494 (m-30) cc_final: 0.8261 (t70) REVERT: E 184 ASP cc_start: 0.8267 (p0) cc_final: 0.8018 (p0) REVERT: E 205 GLU cc_start: 0.8384 (tt0) cc_final: 0.7757 (tm-30) REVERT: E 208 GLN cc_start: 0.8530 (mt0) cc_final: 0.8305 (mt0) REVERT: E 213 LYS cc_start: 0.8034 (tptp) cc_final: 0.7816 (tptp) REVERT: E 216 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 239 ASP cc_start: 0.8766 (m-30) cc_final: 0.8388 (t0) REVERT: E 245 PHE cc_start: 0.8622 (m-80) cc_final: 0.8372 (m-10) REVERT: E 289 GLN cc_start: 0.8911 (mt0) cc_final: 0.7671 (mt0) REVERT: E 413 TYR cc_start: 0.8572 (m-80) cc_final: 0.7612 (m-80) REVERT: F 130 GLU cc_start: 0.9236 (mt-10) cc_final: 0.9024 (mt-10) REVERT: F 261 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.8185 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.6552 time to fit residues: 412.8580 Evaluate side-chains 261 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 195 ASN D 160 ASN F 208 GLN ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16307 Z= 0.234 Angle : 0.595 6.293 22075 Z= 0.321 Chirality : 0.041 0.162 2609 Planarity : 0.004 0.053 2840 Dihedral : 6.577 59.327 2315 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2047 helix: -0.51 (0.16), residues: 881 sheet: -1.24 (0.29), residues: 271 loop : -1.33 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 73 PHE 0.013 0.001 PHE F 298 TYR 0.021 0.001 TYR D 171 ARG 0.010 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8185 (t80) cc_final: 0.7879 (t80) REVERT: A 170 ASP cc_start: 0.9427 (m-30) cc_final: 0.9207 (m-30) REVERT: A 317 LEU cc_start: 0.7077 (mt) cc_final: 0.6750 (mt) REVERT: B 279 ASP cc_start: 0.8665 (m-30) cc_final: 0.8318 (t0) REVERT: B 293 GLU cc_start: 0.9089 (tt0) cc_final: 0.8540 (tm-30) REVERT: B 363 MET cc_start: 0.8639 (mtm) cc_final: 0.8398 (ptp) REVERT: B 393 VAL cc_start: 0.9103 (t) cc_final: 0.8831 (m) REVERT: B 397 VAL cc_start: 0.8645 (t) cc_final: 0.8413 (t) REVERT: C 347 ASP cc_start: 0.8824 (m-30) cc_final: 0.8601 (m-30) REVERT: C 352 ASP cc_start: 0.8855 (p0) cc_final: 0.8539 (p0) REVERT: D 130 GLU cc_start: 0.9154 (tt0) cc_final: 0.8415 (tm-30) REVERT: D 142 MET cc_start: 0.8763 (mtt) cc_final: 0.8366 (mmt) REVERT: D 190 SER cc_start: 0.8794 (t) cc_final: 0.8490 (p) REVERT: D 201 ASP cc_start: 0.8840 (m-30) cc_final: 0.8336 (p0) REVERT: D 256 LYS cc_start: 0.8864 (mttt) cc_final: 0.8620 (mmmt) REVERT: D 285 GLU cc_start: 0.8668 (tp30) cc_final: 0.8450 (tp30) REVERT: D 356 ASP cc_start: 0.8981 (m-30) cc_final: 0.8655 (m-30) REVERT: E 93 TYR cc_start: 0.8058 (t80) cc_final: 0.7791 (t80) REVERT: E 101 ASN cc_start: 0.8532 (m-40) cc_final: 0.7959 (t0) REVERT: E 170 ASP cc_start: 0.8709 (m-30) cc_final: 0.8282 (t70) REVERT: E 239 ASP cc_start: 0.8832 (m-30) cc_final: 0.8517 (t0) REVERT: E 375 ILE cc_start: 0.9532 (tp) cc_final: 0.9327 (tt) REVERT: E 413 TYR cc_start: 0.7857 (m-80) cc_final: 0.7518 (m-80) REVERT: F 182 TYR cc_start: 0.9115 (t80) cc_final: 0.8524 (t80) REVERT: F 247 CYS cc_start: 0.9274 (m) cc_final: 0.8951 (m) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.6012 time to fit residues: 256.7860 Evaluate side-chains 226 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16307 Z= 0.185 Angle : 0.507 5.622 22075 Z= 0.266 Chirality : 0.040 0.152 2609 Planarity : 0.003 0.033 2840 Dihedral : 6.262 57.545 2315 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.17), residues: 2047 helix: -0.10 (0.16), residues: 895 sheet: -0.86 (0.29), residues: 290 loop : -1.19 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 73 PHE 0.007 0.001 PHE A 341 TYR 0.020 0.001 TYR A 93 ARG 0.006 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8215 (t80) cc_final: 0.7919 (t80) REVERT: A 317 LEU cc_start: 0.7114 (mt) cc_final: 0.6762 (mt) REVERT: A 356 ASP cc_start: 0.8324 (t0) cc_final: 0.8048 (p0) REVERT: B 279 ASP cc_start: 0.8705 (m-30) cc_final: 0.8255 (t0) REVERT: B 285 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8855 (mt-10) REVERT: B 293 GLU cc_start: 0.9114 (tt0) cc_final: 0.8732 (tm-30) REVERT: B 347 ASP cc_start: 0.8141 (t70) cc_final: 0.7907 (t0) REVERT: B 393 VAL cc_start: 0.9054 (t) cc_final: 0.8722 (m) REVERT: C 136 LEU cc_start: 0.8810 (tp) cc_final: 0.8523 (tp) REVERT: C 243 ILE cc_start: 0.8961 (mt) cc_final: 0.8678 (mm) REVERT: C 294 ASP cc_start: 0.9169 (m-30) cc_final: 0.8963 (m-30) REVERT: C 320 GLU cc_start: 0.8938 (pp20) cc_final: 0.8569 (pp20) REVERT: C 347 ASP cc_start: 0.8833 (m-30) cc_final: 0.8612 (m-30) REVERT: C 352 ASP cc_start: 0.8934 (p0) cc_final: 0.8628 (p0) REVERT: D 130 GLU cc_start: 0.9130 (tt0) cc_final: 0.8416 (tm-30) REVERT: D 142 MET cc_start: 0.8739 (mtt) cc_final: 0.8312 (mmt) REVERT: D 190 SER cc_start: 0.8742 (t) cc_final: 0.8456 (p) REVERT: D 201 ASP cc_start: 0.8898 (m-30) cc_final: 0.8297 (p0) REVERT: D 256 LYS cc_start: 0.8916 (mttt) cc_final: 0.8566 (mmmt) REVERT: D 356 ASP cc_start: 0.8938 (m-30) cc_final: 0.8617 (m-30) REVERT: E 101 ASN cc_start: 0.8491 (m-40) cc_final: 0.7963 (t0) REVERT: E 144 ASP cc_start: 0.8312 (p0) cc_final: 0.7780 (p0) REVERT: E 170 ASP cc_start: 0.8850 (m-30) cc_final: 0.8349 (t70) REVERT: E 175 LYS cc_start: 0.8956 (tttt) cc_final: 0.8613 (ttpp) REVERT: E 390 MET cc_start: 0.8539 (tpt) cc_final: 0.8176 (tpp) REVERT: E 413 TYR cc_start: 0.8502 (m-80) cc_final: 0.8011 (m-80) REVERT: F 142 MET cc_start: 0.8699 (ttt) cc_final: 0.8438 (tmm) REVERT: F 182 TYR cc_start: 0.9052 (t80) cc_final: 0.8659 (t80) REVERT: F 247 CYS cc_start: 0.9302 (m) cc_final: 0.8998 (m) REVERT: F 293 GLU cc_start: 0.7654 (pm20) cc_final: 0.7249 (pm20) REVERT: F 294 ASP cc_start: 0.8950 (m-30) cc_final: 0.7794 (m-30) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.5643 time to fit residues: 220.4202 Evaluate side-chains 206 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 chunk 125 optimal weight: 0.4980 chunk 187 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN D 260 HIS F 232 GLN ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16307 Z= 0.210 Angle : 0.513 6.282 22075 Z= 0.267 Chirality : 0.040 0.151 2609 Planarity : 0.003 0.025 2840 Dihedral : 6.249 57.504 2315 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.17 % Allowed : 1.05 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.18), residues: 2047 helix: 0.14 (0.17), residues: 892 sheet: -0.64 (0.30), residues: 287 loop : -1.04 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 260 PHE 0.011 0.001 PHE C 245 TYR 0.013 0.001 TYR F 96 ARG 0.003 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8277 (t80) cc_final: 0.7976 (t80) REVERT: A 317 LEU cc_start: 0.7061 (mt) cc_final: 0.6812 (mt) REVERT: B 188 LYS cc_start: 0.8657 (tttt) cc_final: 0.8227 (tttp) REVERT: B 279 ASP cc_start: 0.8678 (m-30) cc_final: 0.8221 (t0) REVERT: B 293 GLU cc_start: 0.9090 (tt0) cc_final: 0.8745 (tm-30) REVERT: B 347 ASP cc_start: 0.8180 (t70) cc_final: 0.7947 (t0) REVERT: B 390 MET cc_start: 0.9071 (mmm) cc_final: 0.8685 (mmm) REVERT: B 393 VAL cc_start: 0.9046 (t) cc_final: 0.8610 (t) REVERT: C 136 LEU cc_start: 0.8848 (tp) cc_final: 0.8538 (tp) REVERT: C 352 ASP cc_start: 0.8900 (p0) cc_final: 0.8554 (p0) REVERT: D 130 GLU cc_start: 0.9142 (tt0) cc_final: 0.8458 (tm-30) REVERT: D 142 MET cc_start: 0.8773 (mtt) cc_final: 0.8342 (mmt) REVERT: D 190 SER cc_start: 0.8824 (t) cc_final: 0.8620 (p) REVERT: D 201 ASP cc_start: 0.8950 (m-30) cc_final: 0.8241 (p0) REVERT: D 256 LYS cc_start: 0.8857 (mttt) cc_final: 0.8648 (mmmt) REVERT: D 286 LEU cc_start: 0.9618 (tp) cc_final: 0.9417 (tt) REVERT: D 356 ASP cc_start: 0.8969 (m-30) cc_final: 0.8641 (m-30) REVERT: E 101 ASN cc_start: 0.8447 (m-40) cc_final: 0.7952 (t0) REVERT: E 135 LEU cc_start: 0.7832 (tp) cc_final: 0.7424 (tt) REVERT: E 144 ASP cc_start: 0.8354 (p0) cc_final: 0.7800 (p0) REVERT: E 170 ASP cc_start: 0.8943 (m-30) cc_final: 0.8411 (t70) REVERT: E 205 GLU cc_start: 0.8608 (tt0) cc_final: 0.8281 (tm-30) REVERT: E 347 ASP cc_start: 0.8453 (m-30) cc_final: 0.8202 (m-30) REVERT: E 387 LEU cc_start: 0.9115 (tp) cc_final: 0.8908 (tt) REVERT: E 390 MET cc_start: 0.8525 (tpt) cc_final: 0.8029 (tpp) REVERT: E 413 TYR cc_start: 0.8538 (m-80) cc_final: 0.8074 (m-80) REVERT: F 182 TYR cc_start: 0.9148 (t80) cc_final: 0.8826 (t80) REVERT: F 247 CYS cc_start: 0.9283 (m) cc_final: 0.8987 (m) REVERT: F 293 GLU cc_start: 0.7529 (pm20) cc_final: 0.7001 (pm20) REVERT: F 294 ASP cc_start: 0.8955 (m-30) cc_final: 0.7945 (m-30) REVERT: F 303 GLU cc_start: 0.7460 (mp0) cc_final: 0.7224 (mp0) outliers start: 3 outliers final: 1 residues processed: 250 average time/residue: 0.6619 time to fit residues: 256.2145 Evaluate side-chains 198 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS D 83 GLN ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16307 Z= 0.260 Angle : 0.552 7.450 22075 Z= 0.285 Chirality : 0.040 0.152 2609 Planarity : 0.003 0.028 2840 Dihedral : 6.376 60.241 2315 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -0.82 (0.18), residues: 2047 helix: 0.03 (0.17), residues: 897 sheet: -0.36 (0.29), residues: 307 loop : -1.12 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 73 PHE 0.015 0.001 PHE B 245 TYR 0.021 0.001 TYR A 337 ARG 0.005 0.000 ARG F 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8357 (t80) cc_final: 0.8057 (t80) REVERT: A 317 LEU cc_start: 0.7069 (mt) cc_final: 0.6809 (mt) REVERT: A 356 ASP cc_start: 0.7997 (p0) cc_final: 0.7683 (p0) REVERT: A 384 MET cc_start: 0.8894 (mpp) cc_final: 0.8323 (mpp) REVERT: B 188 LYS cc_start: 0.8721 (tttt) cc_final: 0.8303 (tttp) REVERT: B 279 ASP cc_start: 0.8747 (m-30) cc_final: 0.8245 (t0) REVERT: B 293 GLU cc_start: 0.9070 (tt0) cc_final: 0.8860 (tm-30) REVERT: B 347 ASP cc_start: 0.8146 (t70) cc_final: 0.7913 (t0) REVERT: B 393 VAL cc_start: 0.9048 (t) cc_final: 0.8655 (m) REVERT: C 136 LEU cc_start: 0.8897 (tp) cc_final: 0.8560 (tp) REVERT: C 352 ASP cc_start: 0.8853 (p0) cc_final: 0.8501 (p0) REVERT: D 130 GLU cc_start: 0.9130 (tt0) cc_final: 0.8372 (tm-30) REVERT: D 142 MET cc_start: 0.8843 (mtt) cc_final: 0.8353 (mmt) REVERT: D 201 ASP cc_start: 0.9112 (m-30) cc_final: 0.8669 (t0) REVERT: D 356 ASP cc_start: 0.8994 (m-30) cc_final: 0.8661 (m-30) REVERT: E 101 ASN cc_start: 0.8496 (m-40) cc_final: 0.7983 (t0) REVERT: E 144 ASP cc_start: 0.8397 (p0) cc_final: 0.7801 (p0) REVERT: E 170 ASP cc_start: 0.9027 (m-30) cc_final: 0.8533 (t0) REVERT: E 347 ASP cc_start: 0.8535 (m-30) cc_final: 0.8299 (m-30) REVERT: E 387 LEU cc_start: 0.9141 (tp) cc_final: 0.8906 (tt) REVERT: E 390 MET cc_start: 0.8622 (tpt) cc_final: 0.8326 (tpp) REVERT: E 413 TYR cc_start: 0.8694 (m-80) cc_final: 0.8209 (m-80) REVERT: F 216 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8067 (tm-30) REVERT: F 247 CYS cc_start: 0.9301 (m) cc_final: 0.9045 (m) REVERT: F 261 ARG cc_start: 0.8104 (ttt-90) cc_final: 0.7568 (ttp80) REVERT: F 294 ASP cc_start: 0.8938 (m-30) cc_final: 0.7962 (m-30) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.5705 time to fit residues: 207.3455 Evaluate side-chains 193 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16307 Z= 0.229 Angle : 0.516 5.682 22075 Z= 0.269 Chirality : 0.040 0.153 2609 Planarity : 0.003 0.027 2840 Dihedral : 6.446 63.040 2315 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -0.73 (0.18), residues: 2047 helix: 0.07 (0.17), residues: 916 sheet: -0.16 (0.29), residues: 307 loop : -1.13 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 95 PHE 0.007 0.001 PHE A 298 TYR 0.013 0.001 TYR F 96 ARG 0.006 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.8598 (m-80) cc_final: 0.8381 (m-80) REVERT: A 317 LEU cc_start: 0.7098 (mt) cc_final: 0.6846 (mt) REVERT: A 384 MET cc_start: 0.8632 (mpp) cc_final: 0.8254 (mpp) REVERT: B 140 PHE cc_start: 0.7865 (t80) cc_final: 0.7651 (t80) REVERT: B 188 LYS cc_start: 0.8734 (tttt) cc_final: 0.8332 (tttp) REVERT: B 279 ASP cc_start: 0.8739 (m-30) cc_final: 0.8193 (t0) REVERT: B 293 GLU cc_start: 0.9053 (tt0) cc_final: 0.8853 (tm-30) REVERT: B 319 GLU cc_start: 0.8587 (pp20) cc_final: 0.8205 (pp20) REVERT: B 347 ASP cc_start: 0.8124 (t70) cc_final: 0.7883 (t0) REVERT: B 363 MET cc_start: 0.8656 (mtt) cc_final: 0.8389 (ptp) REVERT: B 393 VAL cc_start: 0.8959 (t) cc_final: 0.8708 (m) REVERT: C 136 LEU cc_start: 0.9075 (tp) cc_final: 0.8735 (tp) REVERT: C 352 ASP cc_start: 0.8818 (p0) cc_final: 0.8473 (p0) REVERT: D 130 GLU cc_start: 0.9200 (tt0) cc_final: 0.8474 (tm-30) REVERT: D 142 MET cc_start: 0.8872 (mtt) cc_final: 0.8292 (mmt) REVERT: D 356 ASP cc_start: 0.8991 (m-30) cc_final: 0.8647 (m-30) REVERT: E 101 ASN cc_start: 0.8498 (m-40) cc_final: 0.7978 (t0) REVERT: E 135 LEU cc_start: 0.8095 (tt) cc_final: 0.7820 (tp) REVERT: E 144 ASP cc_start: 0.8387 (p0) cc_final: 0.7838 (p0) REVERT: E 170 ASP cc_start: 0.9099 (m-30) cc_final: 0.8553 (t0) REVERT: E 413 TYR cc_start: 0.8739 (m-80) cc_final: 0.8474 (m-80) REVERT: F 247 CYS cc_start: 0.9336 (m) cc_final: 0.9071 (m) REVERT: F 293 GLU cc_start: 0.7490 (pm20) cc_final: 0.6826 (pm20) REVERT: F 294 ASP cc_start: 0.8926 (m-30) cc_final: 0.7950 (m-30) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5437 time to fit residues: 186.5152 Evaluate side-chains 179 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16307 Z= 0.158 Angle : 0.472 5.596 22075 Z= 0.244 Chirality : 0.039 0.153 2609 Planarity : 0.002 0.026 2840 Dihedral : 6.344 64.428 2315 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % 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: -0.39 (0.18), residues: 2047 helix: 0.35 (0.17), residues: 915 sheet: 0.04 (0.30), residues: 304 loop : -0.96 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 95 PHE 0.007 0.001 PHE C 304 TYR 0.013 0.001 TYR F 96 ARG 0.003 0.000 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.8607 (m-80) cc_final: 0.8377 (m-80) REVERT: A 140 PHE cc_start: 0.8312 (t80) cc_final: 0.7989 (t80) REVERT: A 317 LEU cc_start: 0.7018 (mt) cc_final: 0.6754 (mt) REVERT: B 140 PHE cc_start: 0.7827 (t80) cc_final: 0.7577 (t80) REVERT: B 188 LYS cc_start: 0.8623 (tttt) cc_final: 0.8292 (tttp) REVERT: B 293 GLU cc_start: 0.9058 (tt0) cc_final: 0.8857 (tm-30) REVERT: B 347 ASP cc_start: 0.8093 (t70) cc_final: 0.7858 (t0) REVERT: B 363 MET cc_start: 0.8695 (mtt) cc_final: 0.8415 (ptp) REVERT: B 393 VAL cc_start: 0.8951 (t) cc_final: 0.8690 (m) REVERT: C 320 GLU cc_start: 0.8802 (pp20) cc_final: 0.8385 (pp20) REVERT: C 324 GLN cc_start: 0.9251 (mt0) cc_final: 0.8968 (mm110) REVERT: C 352 ASP cc_start: 0.8800 (p0) cc_final: 0.8457 (p0) REVERT: D 130 GLU cc_start: 0.9168 (tt0) cc_final: 0.8461 (tm-30) REVERT: D 142 MET cc_start: 0.8911 (mtt) cc_final: 0.8335 (mmt) REVERT: D 356 ASP cc_start: 0.8962 (m-30) cc_final: 0.8611 (m-30) REVERT: E 101 ASN cc_start: 0.8377 (m-40) cc_final: 0.7824 (t0) REVERT: E 144 ASP cc_start: 0.8386 (p0) cc_final: 0.7821 (p0) REVERT: E 170 ASP cc_start: 0.9110 (m-30) cc_final: 0.8575 (t0) REVERT: E 347 ASP cc_start: 0.8485 (m-30) cc_final: 0.8210 (m-30) REVERT: E 387 LEU cc_start: 0.9164 (tp) cc_final: 0.8933 (tt) REVERT: E 413 TYR cc_start: 0.8792 (m-80) cc_final: 0.8485 (m-80) REVERT: F 247 CYS cc_start: 0.9315 (m) cc_final: 0.9059 (m) REVERT: F 293 GLU cc_start: 0.7521 (pm20) cc_final: 0.6869 (pm20) REVERT: F 294 ASP cc_start: 0.8973 (m-30) cc_final: 0.8086 (m-30) REVERT: F 303 GLU cc_start: 0.7511 (mp0) cc_final: 0.7254 (mp0) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.5562 time to fit residues: 194.3124 Evaluate side-chains 184 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 0.0000 chunk 125 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16307 Z= 0.167 Angle : 0.475 5.582 22075 Z= 0.244 Chirality : 0.039 0.149 2609 Planarity : 0.002 0.032 2840 Dihedral : 6.187 65.629 2315 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 2047 helix: 0.46 (0.17), residues: 915 sheet: 0.22 (0.29), residues: 319 loop : -0.88 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 95 PHE 0.007 0.001 PHE B 245 TYR 0.012 0.001 TYR F 96 ARG 0.004 0.000 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.8606 (m-80) cc_final: 0.8365 (m-80) REVERT: A 315 ASN cc_start: 0.8366 (m-40) cc_final: 0.7900 (t0) REVERT: A 317 LEU cc_start: 0.7010 (mt) cc_final: 0.6276 (mt) REVERT: B 140 PHE cc_start: 0.7859 (t80) cc_final: 0.7575 (t80) REVERT: B 188 LYS cc_start: 0.8591 (tttt) cc_final: 0.8263 (tttp) REVERT: B 347 ASP cc_start: 0.8056 (t70) cc_final: 0.7836 (t0) REVERT: B 363 MET cc_start: 0.8716 (mtt) cc_final: 0.8440 (ptp) REVERT: B 390 MET cc_start: 0.9114 (mmm) cc_final: 0.8771 (tmm) REVERT: B 393 VAL cc_start: 0.8866 (t) cc_final: 0.8431 (t) REVERT: C 320 GLU cc_start: 0.8786 (pp20) cc_final: 0.8363 (pp20) REVERT: C 324 GLN cc_start: 0.9247 (mt0) cc_final: 0.8965 (mm110) REVERT: C 352 ASP cc_start: 0.8824 (p0) cc_final: 0.8491 (p0) REVERT: D 130 GLU cc_start: 0.9202 (tt0) cc_final: 0.8471 (tm-30) REVERT: D 142 MET cc_start: 0.8887 (mtt) cc_final: 0.8162 (mmt) REVERT: D 342 ASN cc_start: 0.9019 (m-40) cc_final: 0.8802 (m110) REVERT: D 356 ASP cc_start: 0.8960 (m-30) cc_final: 0.8604 (m-30) REVERT: E 96 TYR cc_start: 0.8708 (m-80) cc_final: 0.8478 (m-80) REVERT: E 101 ASN cc_start: 0.8336 (m110) cc_final: 0.7786 (t0) REVERT: E 135 LEU cc_start: 0.8209 (tp) cc_final: 0.7724 (tt) REVERT: E 144 ASP cc_start: 0.8395 (p0) cc_final: 0.7817 (p0) REVERT: E 170 ASP cc_start: 0.9125 (m-30) cc_final: 0.8583 (t0) REVERT: E 347 ASP cc_start: 0.8510 (m-30) cc_final: 0.8230 (m-30) REVERT: E 390 MET cc_start: 0.8403 (tpt) cc_final: 0.8107 (tpp) REVERT: E 413 TYR cc_start: 0.8799 (m-80) cc_final: 0.8349 (m-80) REVERT: F 247 CYS cc_start: 0.9295 (m) cc_final: 0.9054 (m) REVERT: F 293 GLU cc_start: 0.7521 (pm20) cc_final: 0.6875 (pm20) REVERT: F 294 ASP cc_start: 0.8976 (m-30) cc_final: 0.8076 (m-30) REVERT: F 303 GLU cc_start: 0.7571 (mp0) cc_final: 0.7311 (mp0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5466 time to fit residues: 186.8438 Evaluate side-chains 185 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 16307 Z= 0.278 Angle : 0.559 7.448 22075 Z= 0.288 Chirality : 0.040 0.172 2609 Planarity : 0.003 0.034 2840 Dihedral : 6.308 68.114 2315 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 2047 helix: 0.04 (0.17), residues: 917 sheet: 0.27 (0.30), residues: 305 loop : -1.09 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 95 PHE 0.010 0.001 PHE A 298 TYR 0.013 0.001 TYR F 96 ARG 0.004 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.8636 (m-80) cc_final: 0.8371 (m-80) REVERT: A 315 ASN cc_start: 0.8375 (m-40) cc_final: 0.7886 (t0) REVERT: B 188 LYS cc_start: 0.8625 (tttt) cc_final: 0.8302 (pttp) REVERT: B 347 ASP cc_start: 0.8131 (t70) cc_final: 0.7901 (t0) REVERT: B 363 MET cc_start: 0.8734 (mtt) cc_final: 0.8372 (ptp) REVERT: B 390 MET cc_start: 0.9155 (mmm) cc_final: 0.8790 (tmm) REVERT: B 393 VAL cc_start: 0.8890 (t) cc_final: 0.8408 (t) REVERT: C 320 GLU cc_start: 0.8740 (pp20) cc_final: 0.8338 (pp20) REVERT: C 324 GLN cc_start: 0.9275 (mt0) cc_final: 0.9061 (mm110) REVERT: C 352 ASP cc_start: 0.8755 (p0) cc_final: 0.8426 (p0) REVERT: D 130 GLU cc_start: 0.9277 (tt0) cc_final: 0.8556 (tm-30) REVERT: D 356 ASP cc_start: 0.9008 (m-30) cc_final: 0.8638 (m-30) REVERT: E 144 ASP cc_start: 0.8388 (p0) cc_final: 0.7829 (p0) REVERT: E 170 ASP cc_start: 0.9139 (m-30) cc_final: 0.8619 (t0) REVERT: E 413 TYR cc_start: 0.8786 (m-80) cc_final: 0.8548 (m-80) REVERT: F 247 CYS cc_start: 0.9299 (m) cc_final: 0.9075 (m) REVERT: F 293 GLU cc_start: 0.7600 (pm20) cc_final: 0.6938 (pm20) REVERT: F 294 ASP cc_start: 0.8931 (m-30) cc_final: 0.7832 (m-30) REVERT: F 303 GLU cc_start: 0.7722 (mp0) cc_final: 0.7467 (mp0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.5534 time to fit residues: 184.7341 Evaluate side-chains 170 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 187 optimal weight: 8.9990 chunk 162 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16307 Z= 0.126 Angle : 0.466 5.654 22075 Z= 0.239 Chirality : 0.039 0.151 2609 Planarity : 0.003 0.032 2840 Dihedral : 6.164 68.592 2315 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 2047 helix: 0.45 (0.17), residues: 923 sheet: 0.40 (0.30), residues: 301 loop : -0.82 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 95 PHE 0.012 0.001 PHE A 245 TYR 0.016 0.001 TYR E 96 ARG 0.005 0.000 ARG B 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.8602 (m-80) cc_final: 0.8353 (m-80) REVERT: A 315 ASN cc_start: 0.8379 (m-40) cc_final: 0.7888 (t0) REVERT: A 317 LEU cc_start: 0.6964 (mt) cc_final: 0.6383 (mt) REVERT: B 188 LYS cc_start: 0.8596 (tttt) cc_final: 0.8329 (tttm) REVERT: B 363 MET cc_start: 0.8688 (mtt) cc_final: 0.8337 (ptp) REVERT: B 390 MET cc_start: 0.9124 (mmm) cc_final: 0.8768 (tmm) REVERT: B 393 VAL cc_start: 0.8875 (t) cc_final: 0.8418 (t) REVERT: C 294 ASP cc_start: 0.9160 (m-30) cc_final: 0.8885 (m-30) REVERT: C 320 GLU cc_start: 0.8718 (pp20) cc_final: 0.8262 (pp20) REVERT: C 352 ASP cc_start: 0.8720 (p0) cc_final: 0.8398 (p0) REVERT: D 130 GLU cc_start: 0.9257 (tt0) cc_final: 0.8527 (tm-30) REVERT: D 201 ASP cc_start: 0.9357 (m-30) cc_final: 0.8791 (t0) REVERT: D 356 ASP cc_start: 0.8960 (m-30) cc_final: 0.8603 (m-30) REVERT: E 101 ASN cc_start: 0.8339 (m110) cc_final: 0.7699 (t0) REVERT: E 144 ASP cc_start: 0.8309 (p0) cc_final: 0.7795 (p0) REVERT: E 170 ASP cc_start: 0.9160 (m-30) cc_final: 0.8633 (t0) REVERT: E 413 TYR cc_start: 0.8799 (m-80) cc_final: 0.8377 (m-80) REVERT: F 247 CYS cc_start: 0.9271 (m) cc_final: 0.9049 (m) REVERT: F 261 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7496 (ttp80) REVERT: F 294 ASP cc_start: 0.8951 (m-30) cc_final: 0.7992 (m-30) REVERT: F 303 GLU cc_start: 0.7750 (mp0) cc_final: 0.7481 (mp0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.5661 time to fit residues: 192.3731 Evaluate side-chains 167 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS C 331 ASN D 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.096578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073518 restraints weight = 157853.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.076998 restraints weight = 70046.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079345 restraints weight = 41701.202| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16307 Z= 0.325 Angle : 0.594 9.235 22075 Z= 0.307 Chirality : 0.040 0.205 2609 Planarity : 0.003 0.035 2840 Dihedral : 6.378 70.192 2315 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.75 (0.18), residues: 2047 helix: -0.10 (0.17), residues: 920 sheet: 0.15 (0.29), residues: 317 loop : -1.10 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 73 PHE 0.012 0.001 PHE E 298 TYR 0.012 0.002 TYR F 96 ARG 0.006 0.001 ARG B 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5999.27 seconds wall clock time: 105 minutes 39.93 seconds (6339.93 seconds total)