Starting phenix.real_space_refine on Fri Mar 22 04:47:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/03_2024/6pp8_20422_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/03_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_20422/03_2024/6pp8_20422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/03_2024/6pp8_20422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/03_2024/6pp8_20422_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp8_20422/03_2024/6pp8_20422_trim_updated.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.39, per 1000 atoms: 0.41 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: 23.82 Conformation dependent library (CDL) restraints added in 3.0 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... running ksdssp... Secondary structure from input PDB file: 109 helices and 16 sheets defined 43.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.20 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 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 82 through 101 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 125 through 135 Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.932A pdb=" N GLU A 216 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 254 through 263 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) Processing helix chain 'A' and resid 292 through 298 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) No H-bonds generated for 'chain 'A' and resid 292 through 298' Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.679A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 352 through 365 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) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.527A pdb=" N LEU A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.697A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.791A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 removed outlier: 3.565A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 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 158 through 169 removed outlier: 3.525A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 186 through 189 removed outlier: 3.577A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.699A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.657A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 292 through 298 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) No H-bonds generated for 'chain 'B' and resid 292 through 298' Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 319 through 327 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 333 through 342 Processing helix chain 'B' and resid 352 through 365 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) Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.686A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.726A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 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 125 through 135 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 169 Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 205 through 216 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 254 through 262 Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.868A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 removed outlier: 3.718A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 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 319 through 325 removed outlier: 3.648A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 342 Processing helix chain 'C' and resid 352 through 365 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) Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.638A pdb=" N ALA C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.543A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 404' Processing helix chain 'D' and resid 67 through 77 removed outlier: 3.706A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 100 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 125 through 135 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 158 through 169 Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'D' and resid 205 through 214 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 254 through 263 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) Processing helix chain 'D' and resid 283 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 292 through 298 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 302 through 306 Processing helix chain 'D' and resid 319 through 325 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) Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 352 through 365 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) Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 83 through 100 Processing helix chain 'E' and resid 125 through 136 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) Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.666A pdb=" N ILE E 161 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 187 through 189 No H-bonds generated for 'chain 'E' and resid 187 through 189' Processing helix chain 'E' and resid 205 through 216 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 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.652A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 298 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 302 through 306 Processing helix chain 'E' and resid 319 through 325 removed outlier: 3.783A pdb=" N ILE E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 342 Processing helix chain 'E' and resid 352 through 365 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 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.739A pdb=" N ALA E 379 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 400 through 404 removed outlier: 3.587A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 404' Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.577A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 101 removed outlier: 3.626A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 136 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 168 removed outlier: 3.544A pdb=" N LEU F 165 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 189 Processing helix chain 'F' and resid 205 through 216 removed outlier: 3.525A pdb=" N GLN F 209 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 212 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS F 213 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 216 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 254 through 261 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 Processing helix chain 'F' and resid 292 through 298 removed outlier: 3.829A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 352 through 365 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 373 through 379 Processing helix chain 'F' and resid 381 through 387 Processing helix chain 'F' and resid 400 through 404 Processing sheet with id= A, first strand: chain 'A' and resid 115 through 117 removed outlier: 3.614A pdb=" N ILE A 115 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 395 through 397 Processing sheet with id= C, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.094A pdb=" N VAL B 310 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE B 118 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA B 312 " --> pdb=" O ILE B 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 140 through 144 removed outlier: 7.115A pdb=" N ILE B 180 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA B 143 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR B 182 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU B 244 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 183 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 246 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, 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) removed outlier: 6.869A pdb=" N ILE B 412 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL B 396 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 410 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 115 through 117 Processing sheet with id= G, first strand: chain 'C' and resid 393 through 397 removed outlier: 7.095A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 115 through 117 Processing sheet with id= I, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.192A pdb=" N ILE D 412 " --> pdb=" O GLU D 394 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.526A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) Processing sheet with id= K, 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= L, first strand: chain 'E' and resid 395 through 397 removed outlier: 3.533A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.571A pdb=" N VAL F 310 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE F 118 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 312 " --> pdb=" O ILE F 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 140 through 144 removed outlier: 7.260A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA F 143 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR F 182 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE F 246 " --> pdb=" O ILE F 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, 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= P, 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) 443 hydrogen bonds defined for protein. 1095 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: 10.93 Time building geometry restraints manager: 24.88 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: 173 2.02 - 2.67: 47936 2.67 - 3.31: 91009 3.31 - 3.96: 111742 3.96 - 4.60: 177690 Nonbonded interactions: 428550 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 428545 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: 0.340 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: 0.510 Extract box with map and model: 3.720 Check model and map are aligned: 0.470 Set scattering table: 0.260 Process input model: 95.050 Find NCS groups from input model: 1.880 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.150 ------------------------------------------------------------------------------- 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= 0.227 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 : 2.387 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: 0.6493 time to fit residues: 408.7061 Evaluate side-chains 261 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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: 3.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16307 Z= 0.261 Angle : 0.579 7.325 22075 Z= 0.308 Chirality : 0.041 0.165 2609 Planarity : 0.004 0.049 2840 Dihedral : 6.500 58.536 2315 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -1.54 (0.17), residues: 2047 helix: -0.59 (0.17), residues: 812 sheet: -1.22 (0.28), residues: 283 loop : -1.23 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 73 PHE 0.016 0.001 PHE F 298 TYR 0.022 0.001 TYR D 171 ARG 0.007 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 278 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.593 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: A 140 PHE cc_start: 0.8222 (t80) cc_final: 0.7948 (t80) REVERT: A 170 ASP cc_start: 0.9409 (m-30) cc_final: 0.9202 (m-30) REVERT: A 317 LEU cc_start: 0.7150 (mt) cc_final: 0.6795 (mt) REVERT: A 356 ASP cc_start: 0.8343 (t0) cc_final: 0.8098 (p0) REVERT: B 279 ASP cc_start: 0.8717 (m-30) cc_final: 0.8348 (t0) REVERT: B 293 GLU cc_start: 0.9096 (tt0) cc_final: 0.8633 (tm-30) REVERT: B 393 VAL cc_start: 0.9092 (t) cc_final: 0.8846 (m) REVERT: B 397 VAL cc_start: 0.8695 (t) cc_final: 0.8451 (t) REVERT: C 136 LEU cc_start: 0.8841 (tp) cc_final: 0.8591 (tp) REVERT: C 347 ASP cc_start: 0.8831 (m-30) cc_final: 0.8581 (m-30) REVERT: C 352 ASP cc_start: 0.8846 (p0) cc_final: 0.8557 (p0) REVERT: D 130 GLU cc_start: 0.9167 (tt0) cc_final: 0.8456 (tm-30) REVERT: D 142 MET cc_start: 0.8773 (mtt) cc_final: 0.8327 (mmt) REVERT: D 190 SER cc_start: 0.8762 (t) cc_final: 0.8498 (p) REVERT: D 201 ASP cc_start: 0.8947 (m-30) cc_final: 0.8282 (p0) REVERT: D 256 LYS cc_start: 0.8918 (mttt) cc_final: 0.8667 (mmmt) REVERT: D 285 GLU cc_start: 0.8748 (tp30) cc_final: 0.8542 (tp30) REVERT: D 356 ASP cc_start: 0.9003 (m-30) cc_final: 0.8708 (m-30) REVERT: E 93 TYR cc_start: 0.8113 (t80) cc_final: 0.7874 (t80) REVERT: E 170 ASP cc_start: 0.8669 (m-30) cc_final: 0.8342 (t70) REVERT: E 239 ASP cc_start: 0.8844 (m-30) cc_final: 0.8494 (t0) REVERT: E 387 LEU cc_start: 0.9172 (tp) cc_final: 0.8972 (tt) REVERT: E 413 TYR cc_start: 0.7906 (m-80) cc_final: 0.7571 (m-80) REVERT: F 142 MET cc_start: 0.8810 (ttt) cc_final: 0.8561 (tmm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.5808 time to fit residues: 242.5868 Evaluate side-chains 228 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.632 ------------------------------------------------------------------------------- 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: 0.4980 chunk 57 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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: 0.7941 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16307 Z= 0.245 Angle : 0.539 7.230 22075 Z= 0.278 Chirality : 0.040 0.156 2609 Planarity : 0.003 0.036 2840 Dihedral : 6.242 55.348 2315 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: -1.35 (0.17), residues: 2047 helix: -0.46 (0.17), residues: 835 sheet: -0.95 (0.28), residues: 303 loop : -1.17 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 73 PHE 0.009 0.001 PHE E 298 TYR 0.024 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 248 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.389 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: 0.8313 (t80) cc_final: 0.8030 (t80) REVERT: A 317 LEU cc_start: 0.7200 (mt) cc_final: 0.6890 (mt) REVERT: B 188 LYS cc_start: 0.8638 (tttt) cc_final: 0.8185 (tttp) REVERT: B 279 ASP cc_start: 0.8694 (m-30) cc_final: 0.8379 (t0) REVERT: B 293 GLU cc_start: 0.9120 (tt0) cc_final: 0.8790 (tm-30) REVERT: B 347 ASP cc_start: 0.8141 (t70) cc_final: 0.7890 (t0) REVERT: B 393 VAL cc_start: 0.9053 (t) cc_final: 0.8733 (m) REVERT: C 136 LEU cc_start: 0.8881 (tp) cc_final: 0.8612 (tp) REVERT: C 352 ASP cc_start: 0.8815 (p0) cc_final: 0.8522 (p0) REVERT: D 130 GLU cc_start: 0.9172 (tt0) cc_final: 0.8478 (tm-30) REVERT: D 142 MET cc_start: 0.8722 (mtt) cc_final: 0.8281 (mmt) REVERT: D 256 LYS cc_start: 0.8973 (mttt) cc_final: 0.8731 (mmmt) REVERT: D 356 ASP cc_start: 0.8989 (m-30) cc_final: 0.8695 (m-30) REVERT: E 101 ASN cc_start: 0.8933 (m-40) cc_final: 0.8653 (m110) REVERT: E 144 ASP cc_start: 0.8369 (p0) cc_final: 0.7832 (p0) REVERT: E 170 ASP cc_start: 0.8851 (m-30) cc_final: 0.8397 (t70) REVERT: E 175 LYS cc_start: 0.9184 (tttt) cc_final: 0.8852 (ttpp) REVERT: E 216 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7759 (tm-30) REVERT: E 247 CYS cc_start: 0.8747 (m) cc_final: 0.8502 (m) REVERT: E 347 ASP cc_start: 0.8422 (m-30) cc_final: 0.8173 (m-30) REVERT: E 390 MET cc_start: 0.8605 (tpt) cc_final: 0.8367 (tpp) REVERT: E 413 TYR cc_start: 0.8666 (m-80) cc_final: 0.8272 (m-80) REVERT: F 142 MET cc_start: 0.8907 (ttt) cc_final: 0.8273 (tmm) REVERT: F 293 GLU cc_start: 0.7836 (pm20) cc_final: 0.7578 (pm20) REVERT: F 294 ASP cc_start: 0.8992 (m-30) cc_final: 0.7972 (m-30) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.5853 time to fit residues: 221.8063 Evaluate side-chains 199 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.538 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 185 GLN 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: 0.7976 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16307 Z= 0.240 Angle : 0.525 7.219 22075 Z= 0.269 Chirality : 0.040 0.162 2609 Planarity : 0.003 0.034 2840 Dihedral : 6.309 59.743 2315 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.12 % Allowed : 1.46 % 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: -1.19 (0.18), residues: 2047 helix: -0.36 (0.17), residues: 841 sheet: -0.72 (0.28), residues: 306 loop : -1.10 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 95 PHE 0.012 0.001 PHE E 298 TYR 0.013 0.001 TYR F 96 ARG 0.004 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 242 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 2.609 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: A 140 PHE cc_start: 0.8388 (t80) cc_final: 0.8059 (t80) REVERT: A 317 LEU cc_start: 0.7158 (mt) cc_final: 0.6855 (mt) REVERT: B 188 LYS cc_start: 0.8703 (tttt) cc_final: 0.8229 (tttp) REVERT: B 279 ASP cc_start: 0.8642 (m-30) cc_final: 0.8364 (t0) REVERT: B 293 GLU cc_start: 0.9135 (tt0) cc_final: 0.8907 (tm-30) REVERT: B 347 ASP cc_start: 0.8193 (t70) cc_final: 0.7983 (t70) REVERT: B 393 VAL cc_start: 0.9012 (t) cc_final: 0.8785 (m) REVERT: C 136 LEU cc_start: 0.8960 (tp) cc_final: 0.8701 (tp) REVERT: C 352 ASP cc_start: 0.8898 (p0) cc_final: 0.8602 (p0) REVERT: D 130 GLU cc_start: 0.9160 (tt0) cc_final: 0.8462 (tm-30) REVERT: D 142 MET cc_start: 0.8769 (mtt) cc_final: 0.8265 (mmt) REVERT: D 256 LYS cc_start: 0.9022 (mttt) cc_final: 0.8787 (mmmt) REVERT: D 286 LEU cc_start: 0.9622 (tp) cc_final: 0.9381 (tt) REVERT: D 356 ASP cc_start: 0.9018 (m-30) cc_final: 0.8722 (m-30) REVERT: E 144 ASP cc_start: 0.8362 (p0) cc_final: 0.7808 (p0) REVERT: E 170 ASP cc_start: 0.8942 (m-30) cc_final: 0.8484 (t70) REVERT: E 247 CYS cc_start: 0.8745 (m) cc_final: 0.8521 (m) REVERT: E 347 ASP cc_start: 0.8493 (m-30) cc_final: 0.8245 (m-30) REVERT: E 387 LEU cc_start: 0.9175 (tp) cc_final: 0.8965 (tt) REVERT: E 390 MET cc_start: 0.8593 (tpt) cc_final: 0.8107 (tpp) REVERT: E 413 TYR cc_start: 0.8625 (m-80) cc_final: 0.8154 (m-80) REVERT: F 142 MET cc_start: 0.8935 (ttt) cc_final: 0.8563 (tmm) REVERT: F 182 TYR cc_start: 0.9044 (t80) cc_final: 0.8620 (t80) REVERT: F 261 ARG cc_start: 0.7949 (ttt-90) cc_final: 0.7457 (ttp80) REVERT: F 294 ASP cc_start: 0.8981 (m-30) cc_final: 0.8130 (m-30) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 0.6019 time to fit residues: 225.5136 Evaluate side-chains 191 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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: 3.9990 chunk 169 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** C 185 GLN C 331 ASN D 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16307 Z= 0.316 Angle : 0.587 8.197 22075 Z= 0.302 Chirality : 0.040 0.165 2609 Planarity : 0.003 0.032 2840 Dihedral : 6.544 64.995 2315 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -1.47 (0.17), residues: 2047 helix: -0.72 (0.17), residues: 852 sheet: -0.59 (0.29), residues: 306 loop : -1.24 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 95 PHE 0.017 0.001 PHE E 298 TYR 0.013 0.002 TYR F 96 ARG 0.006 0.000 ARG E 261 *********************** 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 225 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.422 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: 0.8607 (m-80) cc_final: 0.8361 (m-80) REVERT: B 188 LYS cc_start: 0.8733 (tttt) cc_final: 0.8313 (tttp) REVERT: B 212 LEU cc_start: 0.9193 (mt) cc_final: 0.8971 (mt) REVERT: B 279 ASP cc_start: 0.8661 (m-30) cc_final: 0.8319 (t0) REVERT: B 293 GLU cc_start: 0.9123 (tt0) cc_final: 0.8897 (tm-30) REVERT: B 393 VAL cc_start: 0.9004 (t) cc_final: 0.8764 (m) REVERT: C 136 LEU cc_start: 0.8962 (tp) cc_final: 0.8708 (tp) REVERT: C 352 ASP cc_start: 0.8872 (p0) cc_final: 0.8610 (p0) REVERT: D 130 GLU cc_start: 0.9231 (tt0) cc_final: 0.8486 (tm-30) REVERT: D 142 MET cc_start: 0.8884 (mtt) cc_final: 0.8242 (mmt) REVERT: D 356 ASP cc_start: 0.9044 (m-30) cc_final: 0.8739 (m-30) REVERT: E 93 TYR cc_start: 0.8469 (t80) cc_final: 0.8072 (t80) REVERT: E 135 LEU cc_start: 0.8204 (tp) cc_final: 0.7857 (tt) REVERT: E 144 ASP cc_start: 0.8418 (p0) cc_final: 0.7796 (p0) REVERT: E 170 ASP cc_start: 0.9095 (m-30) cc_final: 0.8663 (t70) REVERT: E 247 CYS cc_start: 0.8767 (m) cc_final: 0.8555 (m) REVERT: E 347 ASP cc_start: 0.8547 (m-30) cc_final: 0.8285 (m-30) REVERT: E 390 MET cc_start: 0.8675 (tpt) cc_final: 0.8398 (tpp) REVERT: E 413 TYR cc_start: 0.8724 (m-80) cc_final: 0.8198 (m-80) REVERT: F 142 MET cc_start: 0.8963 (ttt) cc_final: 0.8647 (tmm) REVERT: F 247 CYS cc_start: 0.9290 (m) cc_final: 0.9057 (m) REVERT: F 293 GLU cc_start: 0.7560 (pm20) cc_final: 0.6874 (pm20) REVERT: F 294 ASP cc_start: 0.8975 (m-30) cc_final: 0.7957 (m-30) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.5599 time to fit residues: 194.8686 Evaluate side-chains 181 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.640 ------------------------------------------------------------------------------- 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: 5.9990 chunk 178 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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: 0.7983 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16307 Z= 0.137 Angle : 0.463 5.529 22075 Z= 0.238 Chirality : 0.039 0.157 2609 Planarity : 0.002 0.027 2840 Dihedral : 6.440 66.521 2315 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2047 helix: -0.22 (0.17), residues: 850 sheet: -0.37 (0.29), residues: 308 loop : -0.90 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 95 PHE 0.006 0.001 PHE C 341 TYR 0.014 0.001 TYR F 96 ARG 0.004 0.000 ARG D 307 *********************** 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 224 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.583 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: 0.8573 (m-80) cc_final: 0.8335 (m-80) REVERT: A 140 PHE cc_start: 0.8377 (t80) cc_final: 0.8032 (t80) REVERT: A 315 ASN cc_start: 0.8364 (m-40) cc_final: 0.7897 (t0) REVERT: A 317 LEU cc_start: 0.7106 (mt) cc_final: 0.6533 (mt) REVERT: B 188 LYS cc_start: 0.8701 (tttt) cc_final: 0.8276 (tttp) REVERT: B 279 ASP cc_start: 0.8612 (m-30) cc_final: 0.8289 (t0) REVERT: B 293 GLU cc_start: 0.9116 (tt0) cc_final: 0.8894 (tm-30) REVERT: B 393 VAL cc_start: 0.8929 (t) cc_final: 0.8726 (m) REVERT: C 352 ASP cc_start: 0.8811 (p0) cc_final: 0.8532 (p0) REVERT: D 130 GLU cc_start: 0.9182 (tt0) cc_final: 0.8390 (tm-30) REVERT: D 142 MET cc_start: 0.8916 (mtt) cc_final: 0.8265 (mmt) REVERT: D 356 ASP cc_start: 0.8991 (m-30) cc_final: 0.8674 (m-30) REVERT: E 93 TYR cc_start: 0.8380 (t80) cc_final: 0.7912 (t80) REVERT: E 101 ASN cc_start: 0.8956 (m-40) cc_final: 0.8729 (m-40) REVERT: E 144 ASP cc_start: 0.8359 (p0) cc_final: 0.7776 (p0) REVERT: E 170 ASP cc_start: 0.9079 (m-30) cc_final: 0.8636 (t70) REVERT: E 205 GLU cc_start: 0.8499 (pp20) cc_final: 0.8206 (pp20) REVERT: E 247 CYS cc_start: 0.8741 (m) cc_final: 0.8520 (m) REVERT: E 347 ASP cc_start: 0.8508 (m-30) cc_final: 0.8238 (m-30) REVERT: E 413 TYR cc_start: 0.8751 (m-80) cc_final: 0.8450 (m-80) REVERT: F 142 MET cc_start: 0.8904 (ttt) cc_final: 0.8575 (tmm) REVERT: F 247 CYS cc_start: 0.9288 (m) cc_final: 0.9069 (m) REVERT: F 261 ARG cc_start: 0.8109 (ttt-90) cc_final: 0.7536 (ttp80) REVERT: F 294 ASP cc_start: 0.8995 (m-30) cc_final: 0.8086 (m-30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.5452 time to fit residues: 190.3432 Evaluate side-chains 182 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.518 ------------------------------------------------------------------------------- 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: 0.7980 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 144 optimal weight: 0.0980 chunk 112 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 0.4980 chunk 197 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16307 Z= 0.151 Angle : 0.461 5.594 22075 Z= 0.234 Chirality : 0.039 0.152 2609 Planarity : 0.002 0.025 2840 Dihedral : 6.308 67.600 2315 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2047 helix: -0.05 (0.18), residues: 857 sheet: -0.16 (0.29), residues: 306 loop : -0.84 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 73 PHE 0.009 0.001 PHE B 245 TYR 0.013 0.001 TYR F 96 ARG 0.002 0.000 ARG F 98 *********************** 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 221 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.494 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: 0.8581 (m-80) cc_final: 0.8335 (m-80) REVERT: A 140 PHE cc_start: 0.8327 (t80) cc_final: 0.8019 (t80) REVERT: A 315 ASN cc_start: 0.8374 (m-40) cc_final: 0.7910 (t0) REVERT: A 317 LEU cc_start: 0.7121 (mt) cc_final: 0.6578 (mt) REVERT: B 188 LYS cc_start: 0.8615 (tttt) cc_final: 0.8246 (tttp) REVERT: B 279 ASP cc_start: 0.8597 (m-30) cc_final: 0.8277 (t0) REVERT: B 293 GLU cc_start: 0.9112 (tt0) cc_final: 0.8894 (tm-30) REVERT: C 294 ASP cc_start: 0.9247 (m-30) cc_final: 0.9036 (m-30) REVERT: C 352 ASP cc_start: 0.8852 (p0) cc_final: 0.8572 (p0) REVERT: D 130 GLU cc_start: 0.9184 (tt0) cc_final: 0.8454 (tm-30) REVERT: D 142 MET cc_start: 0.8920 (mtt) cc_final: 0.8184 (mmt) REVERT: D 356 ASP cc_start: 0.8992 (m-30) cc_final: 0.8661 (m-30) REVERT: E 93 TYR cc_start: 0.8420 (t80) cc_final: 0.7917 (t80) REVERT: E 101 ASN cc_start: 0.8953 (m-40) cc_final: 0.8105 (t0) REVERT: E 135 LEU cc_start: 0.8110 (tt) cc_final: 0.7788 (tp) REVERT: E 144 ASP cc_start: 0.8394 (p0) cc_final: 0.7794 (p0) REVERT: E 170 ASP cc_start: 0.9096 (m-30) cc_final: 0.8651 (t70) REVERT: E 205 GLU cc_start: 0.8483 (pp20) cc_final: 0.8187 (pp20) REVERT: E 247 CYS cc_start: 0.8748 (m) cc_final: 0.8522 (m) REVERT: E 347 ASP cc_start: 0.8470 (m-30) cc_final: 0.8186 (m-30) REVERT: E 413 TYR cc_start: 0.8810 (m-80) cc_final: 0.8461 (m-80) REVERT: F 142 MET cc_start: 0.8894 (ttt) cc_final: 0.8578 (tmm) REVERT: F 247 CYS cc_start: 0.9250 (m) cc_final: 0.9044 (m) REVERT: F 293 GLU cc_start: 0.7623 (pm20) cc_final: 0.7083 (pm20) REVERT: F 294 ASP cc_start: 0.8946 (m-30) cc_final: 0.8081 (m-30) REVERT: F 303 GLU cc_start: 0.7630 (mp0) cc_final: 0.7409 (mp0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5474 time to fit residues: 188.1147 Evaluate side-chains 180 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.548 ------------------------------------------------------------------------------- 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: 5.9990 chunk 78 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5007 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= 0.285 Angle : 0.557 7.870 22075 Z= 0.285 Chirality : 0.040 0.168 2609 Planarity : 0.003 0.037 2840 Dihedral : 6.371 69.501 2315 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2047 helix: -0.50 (0.17), residues: 863 sheet: -0.24 (0.30), residues: 306 loop : -1.11 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 95 PHE 0.015 0.001 PHE E 298 TYR 0.014 0.002 TYR F 96 ARG 0.005 0.000 ARG A 373 *********************** 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 214 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.584 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: 0.8601 (m-80) cc_final: 0.8347 (m-80) REVERT: A 191 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7470 (tpp-160) REVERT: A 315 ASN cc_start: 0.8375 (m-40) cc_final: 0.7896 (t0) REVERT: A 317 LEU cc_start: 0.7160 (mt) cc_final: 0.6640 (mt) REVERT: B 188 LYS cc_start: 0.8597 (tttt) cc_final: 0.8317 (tttm) REVERT: B 279 ASP cc_start: 0.8695 (m-30) cc_final: 0.8296 (t0) REVERT: C 294 ASP cc_start: 0.9247 (m-30) cc_final: 0.9037 (m-30) REVERT: C 352 ASP cc_start: 0.8919 (p0) cc_final: 0.8683 (p0) REVERT: D 130 GLU cc_start: 0.9288 (tt0) cc_final: 0.8562 (tm-30) REVERT: D 205 GLU cc_start: 0.8285 (tt0) cc_final: 0.8068 (tt0) REVERT: D 356 ASP cc_start: 0.9060 (m-30) cc_final: 0.8722 (m-30) REVERT: E 93 TYR cc_start: 0.8428 (t80) cc_final: 0.7930 (t80) REVERT: E 101 ASN cc_start: 0.9012 (m-40) cc_final: 0.8131 (t0) REVERT: E 144 ASP cc_start: 0.8426 (p0) cc_final: 0.7807 (p0) REVERT: E 170 ASP cc_start: 0.9177 (m-30) cc_final: 0.8684 (t70) REVERT: E 205 GLU cc_start: 0.8615 (pp20) cc_final: 0.7847 (pp20) REVERT: E 247 CYS cc_start: 0.8765 (m) cc_final: 0.8563 (m) REVERT: E 347 ASP cc_start: 0.8593 (m-30) cc_final: 0.8323 (m-30) REVERT: F 142 MET cc_start: 0.8961 (ttt) cc_final: 0.8539 (tmm) REVERT: F 159 GLU cc_start: 0.8842 (mp0) cc_final: 0.8597 (mp0) REVERT: F 247 CYS cc_start: 0.9256 (m) cc_final: 0.9028 (m) REVERT: F 261 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7612 (ttp80) REVERT: F 294 ASP cc_start: 0.8975 (m-30) cc_final: 0.7953 (m-30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.5705 time to fit residues: 188.7576 Evaluate side-chains 174 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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: 4.9990 chunk 172 optimal weight: 0.3980 chunk 184 optimal weight: 10.0000 chunk 110 optimal weight: 0.0570 chunk 80 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16307 Z= 0.130 Angle : 0.455 5.617 22075 Z= 0.232 Chirality : 0.039 0.154 2609 Planarity : 0.002 0.031 2840 Dihedral : 6.186 70.077 2315 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: -0.55 (0.18), residues: 2047 helix: 0.01 (0.18), residues: 861 sheet: -0.17 (0.30), residues: 304 loop : -0.66 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 73 PHE 0.007 0.001 PHE A 140 TYR 0.014 0.001 TYR F 96 ARG 0.005 0.000 ARG E 200 *********************** 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 219 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.347 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: 0.8582 (m-80) cc_final: 0.8325 (m-80) REVERT: A 140 PHE cc_start: 0.8290 (t80) cc_final: 0.7993 (t80) REVERT: A 315 ASN cc_start: 0.8377 (m-40) cc_final: 0.7896 (t0) REVERT: A 317 LEU cc_start: 0.7093 (mt) cc_final: 0.6468 (mt) REVERT: B 188 LYS cc_start: 0.8566 (tttt) cc_final: 0.8284 (tttm) REVERT: B 279 ASP cc_start: 0.8668 (m-30) cc_final: 0.8321 (t0) REVERT: C 294 ASP cc_start: 0.9213 (m-30) cc_final: 0.9008 (m-30) REVERT: C 320 GLU cc_start: 0.8835 (pp20) cc_final: 0.8413 (pp20) REVERT: C 352 ASP cc_start: 0.8821 (p0) cc_final: 0.8581 (p0) REVERT: D 130 GLU cc_start: 0.9264 (tt0) cc_final: 0.8484 (tm-30) REVERT: D 286 LEU cc_start: 0.9621 (tp) cc_final: 0.9386 (tp) REVERT: D 356 ASP cc_start: 0.8977 (m-30) cc_final: 0.8642 (m-30) REVERT: E 93 TYR cc_start: 0.8395 (t80) cc_final: 0.7859 (t80) REVERT: E 101 ASN cc_start: 0.8996 (m-40) cc_final: 0.8111 (t0) REVERT: E 144 ASP cc_start: 0.8357 (p0) cc_final: 0.7755 (p0) REVERT: E 170 ASP cc_start: 0.9181 (m-30) cc_final: 0.8652 (t70) REVERT: E 205 GLU cc_start: 0.8458 (pp20) cc_final: 0.7669 (pp20) REVERT: E 347 ASP cc_start: 0.8542 (m-30) cc_final: 0.8265 (m-30) REVERT: E 390 MET cc_start: 0.8395 (tpt) cc_final: 0.8154 (tpp) REVERT: E 413 TYR cc_start: 0.8808 (m-80) cc_final: 0.8396 (m-80) REVERT: F 142 MET cc_start: 0.8929 (ttt) cc_final: 0.8652 (tmm) REVERT: F 159 GLU cc_start: 0.8869 (mp0) cc_final: 0.8659 (mp0) REVERT: F 247 CYS cc_start: 0.9234 (m) cc_final: 0.9020 (m) REVERT: F 261 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7629 (ttp80) REVERT: F 294 ASP cc_start: 0.8975 (m-30) cc_final: 0.8118 (m-30) REVERT: F 342 ASN cc_start: 0.8359 (m-40) cc_final: 0.8121 (m110) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.5671 time to fit residues: 192.1336 Evaluate side-chains 183 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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: 0.9990 chunk 118 optimal weight: 0.0050 chunk 92 optimal weight: 0.0970 chunk 135 optimal weight: 0.9980 chunk 204 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 129 optimal weight: 0.1980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16307 Z= 0.119 Angle : 0.449 5.609 22075 Z= 0.228 Chirality : 0.039 0.148 2609 Planarity : 0.002 0.032 2840 Dihedral : 6.023 70.039 2315 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -0.23 (0.19), residues: 2047 helix: 0.28 (0.18), residues: 861 sheet: 0.11 (0.30), residues: 304 loop : -0.55 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 73 PHE 0.008 0.001 PHE A 245 TYR 0.023 0.001 TYR E 96 ARG 0.005 0.000 ARG E 200 ********************** 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 219 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.767 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 191 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7463 (tpp-160) REVERT: A 315 ASN cc_start: 0.8355 (m-40) cc_final: 0.7888 (t0) REVERT: A 317 LEU cc_start: 0.6986 (mt) cc_final: 0.6365 (mt) REVERT: A 384 MET cc_start: 0.8854 (mtt) cc_final: 0.8374 (mpp) REVERT: B 188 LYS cc_start: 0.8553 (tttt) cc_final: 0.8263 (tttm) REVERT: B 279 ASP cc_start: 0.8512 (m-30) cc_final: 0.8206 (t0) REVERT: B 390 MET cc_start: 0.9106 (mmm) cc_final: 0.8784 (tmm) REVERT: C 159 GLU cc_start: 0.9020 (mp0) cc_final: 0.8473 (mt-10) REVERT: C 320 GLU cc_start: 0.8819 (pp20) cc_final: 0.8357 (pp20) REVERT: C 352 ASP cc_start: 0.8812 (p0) cc_final: 0.8567 (p0) REVERT: D 130 GLU cc_start: 0.9217 (tt0) cc_final: 0.8569 (tm-30) REVERT: D 286 LEU cc_start: 0.9614 (tp) cc_final: 0.9389 (tp) REVERT: D 356 ASP cc_start: 0.8951 (m-30) cc_final: 0.8582 (m-30) REVERT: E 93 TYR cc_start: 0.8381 (t80) cc_final: 0.7793 (t80) REVERT: E 144 ASP cc_start: 0.8326 (p0) cc_final: 0.7769 (p0) REVERT: E 170 ASP cc_start: 0.9155 (m-30) cc_final: 0.8628 (t70) REVERT: E 205 GLU cc_start: 0.8336 (pp20) cc_final: 0.7541 (pp20) REVERT: E 247 CYS cc_start: 0.8743 (m) cc_final: 0.8541 (m) REVERT: E 347 ASP cc_start: 0.8487 (m-30) cc_final: 0.8208 (m-30) REVERT: E 413 TYR cc_start: 0.8812 (m-80) cc_final: 0.8389 (m-80) REVERT: F 142 MET cc_start: 0.8909 (ttt) cc_final: 0.8567 (tmm) REVERT: F 159 GLU cc_start: 0.8864 (mp0) cc_final: 0.8659 (mp0) REVERT: F 261 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7679 (ttp80) REVERT: F 294 ASP cc_start: 0.8977 (m-30) cc_final: 0.8115 (m-30) REVERT: F 342 ASN cc_start: 0.8355 (m-40) cc_final: 0.8113 (m110) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.6067 time to fit residues: 206.5748 Evaluate side-chains 178 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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: 0.9980 chunk 149 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.096987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.073607 restraints weight = 155956.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077119 restraints weight = 70354.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079457 restraints weight = 42553.653| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16307 Z= 0.237 Angle : 0.518 6.928 22075 Z= 0.264 Chirality : 0.039 0.210 2609 Planarity : 0.003 0.032 2840 Dihedral : 6.103 70.498 2315 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -0.63 (0.18), residues: 2047 helix: -0.12 (0.17), residues: 867 sheet: 0.09 (0.30), residues: 306 loop : -0.77 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS E 73 PHE 0.011 0.001 PHE E 298 TYR 0.013 0.001 TYR E 96 ARG 0.004 0.000 ARG E 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6091.79 seconds wall clock time: 108 minutes 27.63 seconds (6507.63 seconds total)