Starting phenix.real_space_refine on Sat Feb 24 03:12:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukp_20808/02_2024/6ukp_20808.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukp_20808/02_2024/6ukp_20808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukp_20808/02_2024/6ukp_20808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukp_20808/02_2024/6ukp_20808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukp_20808/02_2024/6ukp_20808.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukp_20808/02_2024/6ukp_20808.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 84 5.16 5 C 13209 2.51 5 N 3647 2.21 5 O 3759 1.98 5 H 20433 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C ASP 406": "OD1" <-> "OD2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ASP 258": "OD1" <-> "OD2" Residue "D GLU 382": "OE1" <-> "OE2" Residue "D GLU 390": "OE1" <-> "OE2" Residue "D ASP 406": "OD1" <-> "OD2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 189": "OD1" <-> "OD2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E ASP 258": "OD1" <-> "OD2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E GLU 390": "OE1" <-> "OE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "F ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 189": "OD1" <-> "OD2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F ASP 258": "OD1" <-> "OD2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 390": "OE1" <-> "OE2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 189": "OD1" <-> "OD2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ASP 258": "OD1" <-> "OD2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G GLU 390": "OE1" <-> "OE2" Residue "G ASP 406": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41132 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 17.48, per 1000 atoms: 0.42 Number of scatterers: 41132 At special positions: 0 Unit cell: (158.24, 156.52, 118.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 O 3759 8.00 N 3647 7.00 C 13209 6.00 H 20433 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.91 Conformation dependent library (CDL) restraints added in 4.2 seconds 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4802 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 21 sheets defined 44.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.837A pdb=" N ARG A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.617A pdb=" N GLY A 89 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 90 " --> pdb=" O GLU A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.282A pdb=" N PHE A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.664A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.515A pdb=" N LEU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.524A pdb=" N VAL A 272 " --> pdb=" O HIS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.929A pdb=" N ARG A 336 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.768A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 70 " --> pdb=" O TRP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.617A pdb=" N GLY B 89 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 90 " --> pdb=" O GLU B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 90' Processing helix chain 'B' and resid 144 through 160 removed outlier: 4.283A pdb=" N PHE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.665A pdb=" N ILE B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 217' Processing helix chain 'B' and resid 235 through 247 removed outlier: 3.513A pdb=" N LEU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.524A pdb=" N VAL B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG B 336 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 369 removed outlier: 3.768A pdb=" N LEU B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 414 through 417 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR C 47 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C 70 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY C 89 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 90 " --> pdb=" O GLU C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 90' Processing helix chain 'C' and resid 144 through 160 removed outlier: 4.283A pdb=" N PHE C 148 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN C 149 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.665A pdb=" N ILE C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 235 through 247 removed outlier: 3.514A pdb=" N LEU C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 272 removed outlier: 3.523A pdb=" N VAL C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG C 336 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 369 removed outlier: 3.770A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 362 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 369 " --> pdb=" O PHE C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 392 through 401 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 414 through 417 Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR D 47 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS D 70 " --> pdb=" O TRP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY D 89 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 90 " --> pdb=" O GLU D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'D' and resid 144 through 160 removed outlier: 4.282A pdb=" N PHE D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN D 149 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.665A pdb=" N ILE D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 217' Processing helix chain 'D' and resid 235 through 247 removed outlier: 3.514A pdb=" N LEU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 272 removed outlier: 3.524A pdb=" N VAL D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG D 336 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 removed outlier: 3.768A pdb=" N LEU D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 362 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 369 " --> pdb=" O PHE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 392 through 401 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 414 through 417 Processing helix chain 'E' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR E 47 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 70 removed outlier: 3.966A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS E 70 " --> pdb=" O TRP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY E 89 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG E 90 " --> pdb=" O GLU E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 90' Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.283A pdb=" N PHE E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN E 149 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 157 " --> pdb=" O GLU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 removed outlier: 3.664A pdb=" N ILE E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 217' Processing helix chain 'E' and resid 235 through 247 removed outlier: 3.514A pdb=" N LEU E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 272 removed outlier: 3.524A pdb=" N VAL E 272 " --> pdb=" O HIS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 287 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG E 336 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 369 removed outlier: 3.769A pdb=" N LEU E 361 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 362 " --> pdb=" O HIS E 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 369 " --> pdb=" O PHE E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 392 through 401 Processing helix chain 'E' and resid 406 through 413 Processing helix chain 'E' and resid 414 through 417 Processing helix chain 'F' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR F 47 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS F 70 " --> pdb=" O TRP F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY F 89 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'F' and resid 144 through 160 removed outlier: 4.283A pdb=" N PHE F 148 " --> pdb=" O ARG F 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN F 149 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 157 " --> pdb=" O GLU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 217 removed outlier: 3.664A pdb=" N ILE F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 212 through 217' Processing helix chain 'F' and resid 235 through 247 removed outlier: 3.513A pdb=" N LEU F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 272 removed outlier: 3.523A pdb=" N VAL F 272 " --> pdb=" O HIS F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 287 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 333 through 337 removed outlier: 3.927A pdb=" N ARG F 336 " --> pdb=" O TYR F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 369 removed outlier: 3.769A pdb=" N LEU F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR F 362 " --> pdb=" O HIS F 358 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR F 369 " --> pdb=" O PHE F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 392 through 401 Processing helix chain 'F' and resid 406 through 413 Processing helix chain 'F' and resid 414 through 417 Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE G 43 " --> pdb=" O GLY G 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR G 47 " --> pdb=" O PHE G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 70 removed outlier: 3.966A pdb=" N LEU G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG G 69 " --> pdb=" O SER G 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS G 70 " --> pdb=" O TRP G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY G 89 " --> pdb=" O HIS G 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG G 90 " --> pdb=" O GLU G 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 86 through 90' Processing helix chain 'G' and resid 144 through 160 removed outlier: 4.282A pdb=" N PHE G 148 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN G 149 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU G 157 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.836A pdb=" N ASN G 211 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 217 removed outlier: 3.664A pdb=" N ILE G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 212 through 217' Processing helix chain 'G' and resid 235 through 247 removed outlier: 3.513A pdb=" N LEU G 247 " --> pdb=" O LEU G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 272 removed outlier: 3.525A pdb=" N VAL G 272 " --> pdb=" O HIS G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 287 Processing helix chain 'G' and resid 312 through 316 Processing helix chain 'G' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG G 336 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 369 removed outlier: 3.769A pdb=" N LEU G 361 " --> pdb=" O SER G 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 362 " --> pdb=" O HIS G 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR G 369 " --> pdb=" O PHE G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 388 Processing helix chain 'G' and resid 392 through 401 Processing helix chain 'G' and resid 406 through 413 Processing helix chain 'G' and resid 414 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 107 removed outlier: 3.565A pdb=" N GLY A 102 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 51 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N VAL G 79 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 53 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR G 81 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER G 82 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS G 94 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 3.681A pdb=" N LYS A 94 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 82 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 77 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 79 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 102 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR A 169 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER A 255 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ALA A 171 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 282 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER A 277 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE A 328 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 279 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR A 330 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 281 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.848A pdb=" N LEU A 227 " --> pdb=" O GLU A 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 94 through 99 removed outlier: 3.682A pdb=" N LYS B 94 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B 82 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 77 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 53 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 79 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 102 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR B 169 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER B 255 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA B 171 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 282 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER B 277 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE B 328 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 279 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR B 330 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 281 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 226 through 229 removed outlier: 6.849A pdb=" N LEU B 227 " --> pdb=" O GLU B 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 94 through 99 removed outlier: 3.682A pdb=" N LYS C 94 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 82 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C 77 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 79 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 102 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR C 169 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER C 255 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA C 171 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 282 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER C 277 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE C 328 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 279 " --> pdb=" O PHE C 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR C 330 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 281 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.848A pdb=" N LEU C 227 " --> pdb=" O GLU C 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 94 through 99 removed outlier: 3.682A pdb=" N LYS D 94 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER D 82 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU D 77 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 102 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR D 169 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER D 255 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA D 171 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 282 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER D 277 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE D 328 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 279 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR D 330 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU D 281 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 226 through 229 removed outlier: 6.849A pdb=" N LEU D 227 " --> pdb=" O GLU D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 94 through 99 removed outlier: 3.682A pdb=" N LYS E 94 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER E 82 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 77 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 53 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 79 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 102 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR E 169 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N SER E 255 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA E 171 " --> pdb=" O SER E 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU E 282 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER E 277 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE E 328 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL E 279 " --> pdb=" O PHE E 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR E 330 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU E 281 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 226 through 229 removed outlier: 6.849A pdb=" N LEU E 227 " --> pdb=" O GLU E 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 94 through 99 removed outlier: 3.681A pdb=" N LYS F 94 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER F 82 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU F 77 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 79 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY G 102 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR F 169 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER F 255 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ALA F 171 " --> pdb=" O SER F 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU F 282 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER F 277 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE F 328 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 279 " --> pdb=" O PHE F 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR F 330 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU F 281 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.848A pdb=" N LEU F 227 " --> pdb=" O GLU F 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR G 169 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER G 255 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ALA G 171 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU G 282 " --> pdb=" O LEU G 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER G 277 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE G 328 " --> pdb=" O SER G 277 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL G 279 " --> pdb=" O PHE G 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR G 330 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU G 281 " --> pdb=" O THR G 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 226 through 229 removed outlier: 6.849A pdb=" N LEU G 227 " --> pdb=" O GLU G 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 768 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.04 Time building geometry restraints manager: 30.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 20411 1.01 - 1.21: 22 1.21 - 1.41: 8995 1.41 - 1.61: 12068 1.61 - 1.81: 147 Bond restraints: 41643 Sorted by residual: bond pdb=" CG MET G 31 " pdb=" HG2 MET G 31 " ideal model delta sigma weight residual 0.970 1.036 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CD ARG G 33 " pdb=" HD3 ARG G 33 " ideal model delta sigma weight residual 0.970 0.923 0.047 2.00e-02 2.50e+03 5.64e+00 bond pdb=" CD ARG E 33 " pdb=" HD2 ARG E 33 " ideal model delta sigma weight residual 0.970 1.011 -0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" CE MET E 31 " pdb=" HE2 MET E 31 " ideal model delta sigma weight residual 0.970 1.008 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" CD ARG E 33 " pdb=" HD3 ARG E 33 " ideal model delta sigma weight residual 0.970 1.008 -0.038 2.00e-02 2.50e+03 3.62e+00 ... (remaining 41638 not shown) Histogram of bond angle deviations from ideal: 53.17 - 70.93: 4 70.93 - 88.70: 13 88.70 - 106.47: 1141 106.47 - 124.23: 71175 124.23 - 142.00: 2644 Bond angle restraints: 74977 Sorted by residual: angle pdb=" NE ARG G 33 " pdb=" CD ARG G 33 " pdb=" HD3 ARG G 33 " ideal model delta sigma weight residual 108.00 53.17 54.83 3.00e+00 1.11e-01 3.34e+02 angle pdb=" CG ARG G 33 " pdb=" CD ARG G 33 " pdb=" HD3 ARG G 33 " ideal model delta sigma weight residual 109.00 66.49 42.51 3.00e+00 1.11e-01 2.01e+02 angle pdb=" NZ LYS C 34 " pdb=" CE LYS C 34 " pdb=" HE3 LYS C 34 " ideal model delta sigma weight residual 108.00 66.98 41.02 3.00e+00 1.11e-01 1.87e+02 angle pdb=" CD LYS C 34 " pdb=" CE LYS C 34 " pdb=" HE3 LYS C 34 " ideal model delta sigma weight residual 109.00 69.71 39.29 3.00e+00 1.11e-01 1.71e+02 angle pdb=" SD MET E 31 " pdb=" CE MET E 31 " pdb=" HE1 MET E 31 " ideal model delta sigma weight residual 109.00 72.04 36.96 3.00e+00 1.11e-01 1.52e+02 ... (remaining 74972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 17457 17.47 - 34.95: 1588 34.95 - 52.42: 428 52.42 - 69.89: 106 69.89 - 87.36: 28 Dihedral angle restraints: 19607 sinusoidal: 10584 harmonic: 9023 Sorted by residual: dihedral pdb=" CA TYR G 108 " pdb=" C TYR G 108 " pdb=" N GLN G 109 " pdb=" CA GLN G 109 " ideal model delta harmonic sigma weight residual 180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR B 108 " pdb=" C TYR B 108 " pdb=" N GLN B 109 " pdb=" CA GLN B 109 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR C 108 " pdb=" C TYR C 108 " pdb=" N GLN C 109 " pdb=" CA GLN C 109 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 19604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1927 0.037 - 0.074: 836 0.074 - 0.110: 278 0.110 - 0.147: 67 0.147 - 0.184: 14 Chirality restraints: 3122 Sorted by residual: chirality pdb=" CA ILE A 98 " pdb=" N ILE A 98 " pdb=" C ILE A 98 " pdb=" CB ILE A 98 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA ILE D 98 " pdb=" N ILE D 98 " pdb=" C ILE D 98 " pdb=" CB ILE D 98 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA ILE G 98 " pdb=" N ILE G 98 " pdb=" C ILE G 98 " pdb=" CB ILE G 98 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 3119 not shown) Planarity restraints: 6132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 53 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO G 54 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO G 54 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 54 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 53 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO E 54 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO E 54 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 54 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 53 " 0.048 5.00e-02 4.00e+02 7.21e-02 8.32e+00 pdb=" N PRO D 54 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 54 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 54 " 0.040 5.00e-02 4.00e+02 ... (remaining 6129 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1112 2.14 - 2.76: 75371 2.76 - 3.37: 105689 3.37 - 3.99: 126527 3.99 - 4.60: 200887 Nonbonded interactions: 509586 Sorted by model distance: nonbonded pdb=" HE3 LYS C 34 " pdb=" HZ1 LYS C 34 " model vdw 1.530 1.816 nonbonded pdb=" HE2 LYS A 34 " pdb=" HZ1 LYS A 34 " model vdw 1.618 1.816 nonbonded pdb=" HD3 ARG G 33 " pdb=" HE ARG G 33 " model vdw 1.634 1.816 nonbonded pdb=" HD2 LYS C 34 " pdb=" HE3 LYS C 34 " model vdw 1.640 1.952 nonbonded pdb=" O VAL F 384 " pdb=" HG1 THR F 388 " model vdw 1.685 1.850 ... (remaining 509581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.510 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: 0.590 Extract box with map and model: 3.810 Check model and map are aligned: 0.610 Set scattering table: 0.430 Process input model: 116.330 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.008 0.082 21210 Z= 0.520 Angle : 0.867 14.521 28763 Z= 0.443 Chirality : 0.046 0.184 3122 Planarity : 0.006 0.072 3696 Dihedral : 14.311 87.363 7805 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 0.95 % Allowed : 3.89 % Favored : 95.16 % 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: -4.02 (0.15), residues: 2541 helix: -2.24 (0.13), residues: 931 sheet: -2.62 (0.18), residues: 595 loop : -2.91 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 214 HIS 0.009 0.002 HIS B 86 PHE 0.016 0.002 PHE D 400 TYR 0.018 0.002 TYR D 60 ARG 0.005 0.001 ARG E 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 555 time to evaluate : 3.451 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.5917 (m-80) cc_final: 0.5092 (m-80) REVERT: A 80 GLU cc_start: 0.6908 (tt0) cc_final: 0.6575 (mt-10) REVERT: A 92 SER cc_start: 0.8521 (m) cc_final: 0.8318 (t) REVERT: A 132 TRP cc_start: 0.7194 (t60) cc_final: 0.5652 (t-100) REVERT: A 168 MET cc_start: 0.7856 (tpp) cc_final: 0.7475 (tpp) REVERT: A 189 ASP cc_start: 0.8612 (m-30) cc_final: 0.8024 (p0) REVERT: A 222 TYR cc_start: 0.7490 (t80) cc_final: 0.6949 (t80) REVERT: A 227 LEU cc_start: 0.9046 (tt) cc_final: 0.8743 (tp) REVERT: A 360 GLN cc_start: 0.7964 (tt0) cc_final: 0.7720 (tt0) REVERT: A 379 ASN cc_start: 0.7771 (t0) cc_final: 0.7387 (t0) REVERT: A 413 ASN cc_start: 0.7045 (m110) cc_final: 0.6644 (m110) REVERT: B 80 GLU cc_start: 0.7382 (tt0) cc_final: 0.6970 (mt-10) REVERT: B 98 ILE cc_start: 0.8235 (mt) cc_final: 0.7996 (mm) REVERT: B 116 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 162 GLU cc_start: 0.7424 (tp30) cc_final: 0.7143 (tp30) REVERT: B 189 ASP cc_start: 0.8817 (m-30) cc_final: 0.8203 (p0) REVERT: B 248 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7697 (mm-30) REVERT: B 360 GLN cc_start: 0.7779 (tt0) cc_final: 0.7533 (tt0) REVERT: B 413 ASN cc_start: 0.7775 (m110) cc_final: 0.7540 (m110) REVERT: C 45 ARG cc_start: 0.6965 (mmp-170) cc_final: 0.5175 (ptm160) REVERT: C 77 LEU cc_start: 0.7565 (pt) cc_final: 0.7331 (pp) REVERT: C 116 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 125 ASP cc_start: 0.6920 (m-30) cc_final: 0.6482 (t0) REVERT: C 133 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 189 ASP cc_start: 0.8848 (m-30) cc_final: 0.8183 (p0) REVERT: C 222 TYR cc_start: 0.7550 (t80) cc_final: 0.7239 (t80) REVERT: C 325 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8301 (ttt-90) REVERT: C 359 TRP cc_start: 0.7885 (t60) cc_final: 0.7560 (t-100) REVERT: C 379 ASN cc_start: 0.8324 (t0) cc_final: 0.7948 (t0) REVERT: C 382 GLU cc_start: 0.8179 (tp30) cc_final: 0.7867 (tp30) REVERT: C 408 MET cc_start: 0.8135 (mtt) cc_final: 0.7774 (mtt) REVERT: D 31 MET cc_start: -0.0223 (OUTLIER) cc_final: -0.0574 (mpp) REVERT: D 45 ARG cc_start: 0.7015 (mmp-170) cc_final: 0.5061 (ttm170) REVERT: D 80 GLU cc_start: 0.7290 (tt0) cc_final: 0.6809 (mt-10) REVERT: D 96 GLU cc_start: 0.5962 (tt0) cc_final: 0.5681 (tt0) REVERT: D 181 TYR cc_start: 0.8071 (m-10) cc_final: 0.7761 (m-80) REVERT: D 189 ASP cc_start: 0.8554 (m-30) cc_final: 0.7942 (p0) REVERT: D 379 ASN cc_start: 0.7783 (t0) cc_final: 0.7425 (t0) REVERT: E 47 TYR cc_start: 0.5947 (m-80) cc_final: 0.5525 (m-80) REVERT: E 77 LEU cc_start: 0.7689 (pt) cc_final: 0.7436 (pp) REVERT: E 80 GLU cc_start: 0.6825 (tt0) cc_final: 0.6583 (mt-10) REVERT: E 92 SER cc_start: 0.8374 (m) cc_final: 0.7925 (t) REVERT: E 116 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6968 (mt-10) REVERT: E 145 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7485 (tptp) REVERT: E 189 ASP cc_start: 0.8550 (m-30) cc_final: 0.7532 (p0) REVERT: E 223 ARG cc_start: 0.7729 (ttm170) cc_final: 0.7038 (mtm180) REVERT: E 234 CYS cc_start: 0.8453 (t) cc_final: 0.8071 (t) REVERT: E 401 MET cc_start: 0.7426 (ttt) cc_final: 0.7040 (ttt) REVERT: E 404 LYS cc_start: 0.7273 (mmtt) cc_final: 0.6895 (mmtt) REVERT: E 413 ASN cc_start: 0.8059 (m110) cc_final: 0.7715 (m110) REVERT: F 31 MET cc_start: 0.1880 (OUTLIER) cc_final: 0.1352 (mtm) REVERT: F 45 ARG cc_start: 0.7088 (mmp-170) cc_final: 0.5246 (ttp-170) REVERT: F 47 TYR cc_start: 0.6318 (m-80) cc_final: 0.4917 (m-80) REVERT: F 49 ILE cc_start: 0.8020 (mt) cc_final: 0.7783 (tt) REVERT: F 80 GLU cc_start: 0.7275 (tt0) cc_final: 0.6978 (mt-10) REVERT: F 98 ILE cc_start: 0.8456 (mt) cc_final: 0.8204 (mm) REVERT: F 108 TYR cc_start: 0.8276 (t80) cc_final: 0.8032 (t80) REVERT: F 134 SER cc_start: 0.8291 (m) cc_final: 0.8080 (t) REVERT: F 143 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: F 162 GLU cc_start: 0.6946 (tp30) cc_final: 0.6744 (tp30) REVERT: F 177 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7221 (mtt-85) REVERT: F 189 ASP cc_start: 0.8682 (m-30) cc_final: 0.7974 (p0) REVERT: F 213 LYS cc_start: 0.8131 (tptp) cc_final: 0.7443 (tptp) REVERT: F 223 ARG cc_start: 0.7449 (ttm170) cc_final: 0.7225 (ttp-110) REVERT: F 234 CYS cc_start: 0.8072 (t) cc_final: 0.7780 (t) REVERT: F 279 VAL cc_start: 0.8622 (m) cc_final: 0.8276 (p) REVERT: F 325 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8079 (tmm160) REVERT: F 356 CYS cc_start: 0.8139 (m) cc_final: 0.7830 (m) REVERT: F 365 PHE cc_start: 0.7718 (t80) cc_final: 0.7328 (t80) REVERT: F 390 GLU cc_start: 0.8309 (pm20) cc_final: 0.7908 (pm20) REVERT: F 413 ASN cc_start: 0.7895 (m110) cc_final: 0.7543 (m110) REVERT: G 31 MET cc_start: 0.0590 (OUTLIER) cc_final: 0.0119 (mpp) REVERT: G 45 ARG cc_start: 0.7062 (mmp-170) cc_final: 0.6323 (mmm160) REVERT: G 47 TYR cc_start: 0.6570 (m-80) cc_final: 0.5250 (m-80) REVERT: G 116 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7249 (mt-10) REVERT: G 134 SER cc_start: 0.8362 (m) cc_final: 0.7982 (p) REVERT: G 177 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7816 (mmm-85) REVERT: G 189 ASP cc_start: 0.8824 (m-30) cc_final: 0.8203 (p0) REVERT: G 217 ASP cc_start: 0.8148 (m-30) cc_final: 0.7830 (m-30) REVERT: G 356 CYS cc_start: 0.7679 (m) cc_final: 0.7346 (m) REVERT: G 413 ASN cc_start: 0.8472 (m110) cc_final: 0.8178 (m110) outliers start: 21 outliers final: 3 residues processed: 556 average time/residue: 0.9130 time to fit residues: 714.9544 Evaluate side-chains 460 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 453 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain G residue 31 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 228 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS B 46 HIS B 412 HIS C 412 HIS D 412 HIS D 413 ASN E 412 HIS F 412 HIS G 412 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21210 Z= 0.190 Angle : 0.544 5.563 28763 Z= 0.285 Chirality : 0.038 0.172 3122 Planarity : 0.005 0.064 3696 Dihedral : 5.836 59.453 2887 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.95 % Allowed : 12.21 % Favored : 86.84 % 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: -2.70 (0.16), residues: 2541 helix: -0.69 (0.16), residues: 952 sheet: -1.75 (0.20), residues: 567 loop : -2.82 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 132 HIS 0.006 0.001 HIS F 86 PHE 0.016 0.002 PHE F 179 TYR 0.014 0.001 TYR G 83 ARG 0.005 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 464 time to evaluate : 3.621 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6028 (m-80) cc_final: 0.5537 (m-80) REVERT: A 80 GLU cc_start: 0.6963 (tt0) cc_final: 0.6645 (mt-10) REVERT: A 92 SER cc_start: 0.8646 (m) cc_final: 0.8315 (t) REVERT: A 186 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8270 (ptp90) REVERT: A 189 ASP cc_start: 0.8565 (m-30) cc_final: 0.7935 (p0) REVERT: A 222 TYR cc_start: 0.7472 (t80) cc_final: 0.6937 (t80) REVERT: A 323 GLU cc_start: 0.7804 (pm20) cc_final: 0.7539 (pm20) REVERT: A 379 ASN cc_start: 0.7741 (t0) cc_final: 0.7363 (t0) REVERT: B 47 TYR cc_start: 0.5953 (m-80) cc_final: 0.5064 (m-80) REVERT: B 80 GLU cc_start: 0.7469 (tt0) cc_final: 0.6998 (mt-10) REVERT: B 113 ILE cc_start: 0.8271 (mt) cc_final: 0.8056 (mm) REVERT: B 177 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7178 (mtt-85) REVERT: B 218 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7295 (mtm180) REVERT: B 248 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 332 ASN cc_start: 0.8559 (m-40) cc_final: 0.8337 (m-40) REVERT: B 360 GLN cc_start: 0.7784 (tt0) cc_final: 0.7415 (tt0) REVERT: B 382 GLU cc_start: 0.7797 (tp30) cc_final: 0.7474 (tp30) REVERT: B 413 ASN cc_start: 0.7676 (m110) cc_final: 0.7434 (m110) REVERT: C 133 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7706 (mt-10) REVERT: C 168 MET cc_start: 0.8193 (tpp) cc_final: 0.7960 (tpp) REVERT: C 189 ASP cc_start: 0.8896 (m-30) cc_final: 0.8242 (p0) REVERT: C 218 ARG cc_start: 0.8398 (mmt90) cc_final: 0.8128 (mtm180) REVERT: C 222 TYR cc_start: 0.7535 (t80) cc_final: 0.7238 (t80) REVERT: C 240 ILE cc_start: 0.8612 (mm) cc_final: 0.8383 (mm) REVERT: C 359 TRP cc_start: 0.7870 (t60) cc_final: 0.7517 (t-100) REVERT: C 379 ASN cc_start: 0.8224 (t0) cc_final: 0.7841 (t0) REVERT: C 382 GLU cc_start: 0.8013 (tp30) cc_final: 0.7578 (tp30) REVERT: C 408 MET cc_start: 0.8092 (mtt) cc_final: 0.7727 (mtt) REVERT: D 31 MET cc_start: -0.0113 (OUTLIER) cc_final: -0.0432 (mpp) REVERT: D 80 GLU cc_start: 0.7190 (tt0) cc_final: 0.6808 (mt-10) REVERT: D 116 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6949 (mt-10) REVERT: D 189 ASP cc_start: 0.8577 (m-30) cc_final: 0.7990 (p0) REVERT: D 379 ASN cc_start: 0.7685 (t0) cc_final: 0.7373 (t0) REVERT: E 47 TYR cc_start: 0.5838 (m-80) cc_final: 0.5574 (m-80) REVERT: E 80 GLU cc_start: 0.6966 (tt0) cc_final: 0.6733 (mt-10) REVERT: E 92 SER cc_start: 0.8399 (m) cc_final: 0.8135 (t) REVERT: E 116 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6907 (mt-10) REVERT: E 189 ASP cc_start: 0.8445 (m-30) cc_final: 0.7565 (p0) REVERT: E 223 ARG cc_start: 0.7511 (ttm170) cc_final: 0.7044 (mtm180) REVERT: E 401 MET cc_start: 0.7696 (ttt) cc_final: 0.7228 (ttt) REVERT: E 404 LYS cc_start: 0.7091 (mmtt) cc_final: 0.6872 (mmtt) REVERT: F 47 TYR cc_start: 0.6488 (m-80) cc_final: 0.5317 (m-80) REVERT: F 49 ILE cc_start: 0.7979 (mt) cc_final: 0.7626 (tt) REVERT: F 73 ARG cc_start: 0.7551 (mmt180) cc_final: 0.7130 (mmt180) REVERT: F 80 GLU cc_start: 0.7588 (tt0) cc_final: 0.7271 (mt-10) REVERT: F 98 ILE cc_start: 0.8541 (mt) cc_final: 0.8249 (mm) REVERT: F 162 GLU cc_start: 0.7027 (tp30) cc_final: 0.6735 (tp30) REVERT: F 177 ARG cc_start: 0.7751 (mmm-85) cc_final: 0.7351 (mmt90) REVERT: F 189 ASP cc_start: 0.8681 (m-30) cc_final: 0.7967 (p0) REVERT: F 234 CYS cc_start: 0.7903 (t) cc_final: 0.7540 (t) REVERT: F 279 VAL cc_start: 0.8819 (m) cc_final: 0.8440 (p) REVERT: F 378 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8179 (mt-10) REVERT: F 390 GLU cc_start: 0.8273 (pm20) cc_final: 0.8073 (pm20) REVERT: G 31 MET cc_start: 0.0765 (OUTLIER) cc_final: 0.0302 (mpp) REVERT: G 45 ARG cc_start: 0.7291 (mmp-170) cc_final: 0.5717 (ttp-170) REVERT: G 47 TYR cc_start: 0.6170 (m-80) cc_final: 0.4990 (m-80) REVERT: G 123 MET cc_start: 0.6096 (ptm) cc_final: 0.5866 (ptm) REVERT: G 177 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7833 (mmm-85) REVERT: G 189 ASP cc_start: 0.8821 (m-30) cc_final: 0.8205 (p0) REVERT: G 217 ASP cc_start: 0.8086 (m-30) cc_final: 0.7732 (m-30) REVERT: G 391 ILE cc_start: 0.8045 (pt) cc_final: 0.7830 (pt) REVERT: G 413 ASN cc_start: 0.8419 (m110) cc_final: 0.8124 (m110) outliers start: 21 outliers final: 16 residues processed: 469 average time/residue: 0.8968 time to fit residues: 592.5070 Evaluate side-chains 456 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 438 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain G residue 31 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN B 46 HIS C 413 ASN E 413 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21210 Z= 0.219 Angle : 0.520 5.497 28763 Z= 0.276 Chirality : 0.038 0.167 3122 Planarity : 0.005 0.064 3696 Dihedral : 5.231 55.150 2878 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 1.45 % Allowed : 13.70 % Favored : 84.86 % 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: -1.99 (0.17), residues: 2541 helix: 0.20 (0.17), residues: 952 sheet: -1.47 (0.21), residues: 560 loop : -2.70 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 132 HIS 0.010 0.001 HIS B 46 PHE 0.018 0.002 PHE F 179 TYR 0.030 0.001 TYR B 47 ARG 0.012 0.001 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 441 time to evaluate : 3.430 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.5994 (m-80) cc_final: 0.5490 (m-80) REVERT: A 80 GLU cc_start: 0.6956 (tt0) cc_final: 0.6668 (mt-10) REVERT: A 92 SER cc_start: 0.8712 (m) cc_final: 0.8298 (t) REVERT: A 186 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8275 (ptp90) REVERT: A 189 ASP cc_start: 0.8408 (m-30) cc_final: 0.7906 (p0) REVERT: A 323 GLU cc_start: 0.7980 (pm20) cc_final: 0.7742 (pm20) REVERT: A 379 ASN cc_start: 0.7790 (t0) cc_final: 0.7389 (t0) REVERT: B 47 TYR cc_start: 0.5776 (m-80) cc_final: 0.5059 (m-80) REVERT: B 113 ILE cc_start: 0.8229 (mt) cc_final: 0.8019 (mm) REVERT: B 177 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7169 (mtt-85) REVERT: B 217 ASP cc_start: 0.7402 (m-30) cc_final: 0.7004 (m-30) REVERT: B 223 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7472 (ttp-110) REVERT: B 248 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7564 (mm-30) REVERT: B 360 GLN cc_start: 0.7875 (tt0) cc_final: 0.7249 (tt0) REVERT: B 382 GLU cc_start: 0.7801 (tp30) cc_final: 0.7455 (tp30) REVERT: C 189 ASP cc_start: 0.9006 (m-30) cc_final: 0.8161 (p0) REVERT: C 222 TYR cc_start: 0.7526 (t80) cc_final: 0.7289 (t80) REVERT: C 240 ILE cc_start: 0.8624 (mm) cc_final: 0.8387 (mm) REVERT: C 359 TRP cc_start: 0.7974 (t60) cc_final: 0.7639 (t-100) REVERT: C 379 ASN cc_start: 0.7963 (t0) cc_final: 0.7662 (t0) REVERT: C 382 GLU cc_start: 0.8067 (tp30) cc_final: 0.7818 (tp30) REVERT: C 390 GLU cc_start: 0.8476 (pm20) cc_final: 0.8065 (pm20) REVERT: C 408 MET cc_start: 0.8050 (mtt) cc_final: 0.7682 (mtt) REVERT: D 31 MET cc_start: 0.0051 (OUTLIER) cc_final: -0.0343 (mpp) REVERT: D 80 GLU cc_start: 0.7139 (tt0) cc_final: 0.6775 (mt-10) REVERT: D 168 MET cc_start: 0.8005 (ttm) cc_final: 0.7763 (ttm) REVERT: D 189 ASP cc_start: 0.8379 (m-30) cc_final: 0.7935 (p0) REVERT: D 379 ASN cc_start: 0.7673 (t0) cc_final: 0.7420 (t0) REVERT: E 80 GLU cc_start: 0.7118 (tt0) cc_final: 0.6863 (mt-10) REVERT: E 92 SER cc_start: 0.8362 (m) cc_final: 0.8065 (t) REVERT: E 116 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7012 (mt-10) REVERT: E 165 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8351 (mmtp) REVERT: E 177 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7268 (mmt90) REVERT: E 189 ASP cc_start: 0.8418 (m-30) cc_final: 0.7563 (p0) REVERT: E 223 ARG cc_start: 0.7586 (ttm170) cc_final: 0.7255 (mtm180) REVERT: E 390 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: E 401 MET cc_start: 0.7916 (ttt) cc_final: 0.7524 (ttt) REVERT: F 73 ARG cc_start: 0.7576 (mmt180) cc_final: 0.7174 (mmt180) REVERT: F 80 GLU cc_start: 0.7673 (tt0) cc_final: 0.7272 (mt-10) REVERT: F 98 ILE cc_start: 0.8886 (mt) cc_final: 0.8675 (mm) REVERT: F 108 TYR cc_start: 0.7933 (t80) cc_final: 0.7287 (t80) REVERT: F 177 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7358 (mmt90) REVERT: F 189 ASP cc_start: 0.8603 (m-30) cc_final: 0.7832 (p0) REVERT: F 234 CYS cc_start: 0.7802 (t) cc_final: 0.7466 (t) REVERT: F 378 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8762 (mt-10) REVERT: G 45 ARG cc_start: 0.7371 (mmp-170) cc_final: 0.5287 (ttp-170) REVERT: G 47 TYR cc_start: 0.6238 (m-80) cc_final: 0.5162 (m-80) REVERT: G 177 ARG cc_start: 0.7849 (mmm-85) cc_final: 0.7605 (mmm-85) REVERT: G 189 ASP cc_start: 0.8829 (m-30) cc_final: 0.8175 (p0) REVERT: G 217 ASP cc_start: 0.8057 (m-30) cc_final: 0.7674 (m-30) REVERT: G 413 ASN cc_start: 0.8017 (m110) cc_final: 0.7763 (m110) outliers start: 32 outliers final: 21 residues processed: 453 average time/residue: 0.9108 time to fit residues: 592.6628 Evaluate side-chains 449 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 426 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.3980 chunk 172 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21210 Z= 0.205 Angle : 0.504 6.167 28763 Z= 0.267 Chirality : 0.038 0.169 3122 Planarity : 0.005 0.063 3696 Dihedral : 4.949 50.047 2873 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.54 % Allowed : 15.05 % Favored : 83.41 % 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: -1.51 (0.18), residues: 2541 helix: 0.63 (0.17), residues: 959 sheet: -1.18 (0.21), residues: 560 loop : -2.51 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 132 HIS 0.010 0.001 HIS B 46 PHE 0.018 0.002 PHE A 368 TYR 0.014 0.001 TYR G 83 ARG 0.006 0.001 ARG F 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 439 time to evaluate : 3.319 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6965 (tt0) cc_final: 0.6606 (mt-10) REVERT: A 92 SER cc_start: 0.9176 (m) cc_final: 0.8624 (t) REVERT: A 186 ARG cc_start: 0.8576 (mtt180) cc_final: 0.8221 (ptp90) REVERT: A 189 ASP cc_start: 0.8412 (m-30) cc_final: 0.7866 (p0) REVERT: A 379 ASN cc_start: 0.7556 (t0) cc_final: 0.7227 (t0) REVERT: B 46 HIS cc_start: 0.6955 (t-170) cc_final: 0.6635 (t70) REVERT: B 47 TYR cc_start: 0.5248 (m-80) cc_final: 0.4075 (m-80) REVERT: B 177 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.7174 (mtt-85) REVERT: B 217 ASP cc_start: 0.7578 (m-30) cc_final: 0.6965 (m-30) REVERT: B 248 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 360 GLN cc_start: 0.7751 (tt0) cc_final: 0.7316 (tt0) REVERT: B 382 GLU cc_start: 0.7794 (tp30) cc_final: 0.7444 (tp30) REVERT: B 401 MET cc_start: 0.8293 (tpt) cc_final: 0.7252 (tpt) REVERT: C 161 GLN cc_start: 0.7030 (mt0) cc_final: 0.6826 (mt0) REVERT: C 189 ASP cc_start: 0.8894 (m-30) cc_final: 0.8286 (p0) REVERT: C 240 ILE cc_start: 0.8605 (mm) cc_final: 0.8405 (mm) REVERT: C 325 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8348 (tmm-80) REVERT: C 359 TRP cc_start: 0.8025 (t60) cc_final: 0.7698 (t-100) REVERT: C 379 ASN cc_start: 0.8002 (t0) cc_final: 0.7716 (t0) REVERT: C 382 GLU cc_start: 0.8058 (tp30) cc_final: 0.7579 (tp30) REVERT: C 390 GLU cc_start: 0.8640 (pm20) cc_final: 0.8159 (pm20) REVERT: C 408 MET cc_start: 0.8017 (mtt) cc_final: 0.7645 (mtt) REVERT: D 80 GLU cc_start: 0.7133 (tt0) cc_final: 0.6712 (mt-10) REVERT: D 189 ASP cc_start: 0.8381 (m-30) cc_final: 0.7887 (p0) REVERT: D 248 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7820 (mm-30) REVERT: D 379 ASN cc_start: 0.7702 (t0) cc_final: 0.7427 (t0) REVERT: E 80 GLU cc_start: 0.7069 (tt0) cc_final: 0.6853 (mt-10) REVERT: E 92 SER cc_start: 0.8413 (m) cc_final: 0.8143 (t) REVERT: E 94 LYS cc_start: 0.8470 (tttp) cc_final: 0.8153 (tttt) REVERT: E 116 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7105 (mt-10) REVERT: E 189 ASP cc_start: 0.8430 (m-30) cc_final: 0.7593 (p0) REVERT: E 390 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8250 (pm20) REVERT: E 401 MET cc_start: 0.7746 (ttt) cc_final: 0.7401 (ttt) REVERT: F 73 ARG cc_start: 0.7392 (mmt180) cc_final: 0.6973 (mmt180) REVERT: F 80 GLU cc_start: 0.7689 (tt0) cc_final: 0.7282 (mt-10) REVERT: F 98 ILE cc_start: 0.8961 (mt) cc_final: 0.8727 (mm) REVERT: F 116 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6566 (mt-10) REVERT: F 134 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8360 (p) REVERT: F 177 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7268 (mtt-85) REVERT: F 234 CYS cc_start: 0.7691 (t) cc_final: 0.7367 (t) REVERT: F 365 PHE cc_start: 0.6982 (t80) cc_final: 0.6513 (t80) REVERT: F 390 GLU cc_start: 0.8119 (pm20) cc_final: 0.7643 (pm20) REVERT: G 45 ARG cc_start: 0.7420 (mmp-170) cc_final: 0.5329 (ttp-170) REVERT: G 47 TYR cc_start: 0.6309 (m-80) cc_final: 0.5224 (m-80) REVERT: G 98 ILE cc_start: 0.9007 (mm) cc_final: 0.8750 (mt) REVERT: G 177 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7611 (mmm-85) REVERT: G 189 ASP cc_start: 0.8837 (m-30) cc_final: 0.8210 (p0) REVERT: G 217 ASP cc_start: 0.8018 (m-30) cc_final: 0.7624 (m-30) REVERT: G 413 ASN cc_start: 0.8031 (m110) cc_final: 0.7772 (m110) outliers start: 34 outliers final: 30 residues processed: 452 average time/residue: 0.8439 time to fit residues: 546.8470 Evaluate side-chains 456 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 424 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 TYR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.003 0.023 21210 Z= 0.167 Angle : 0.482 6.911 28763 Z= 0.254 Chirality : 0.037 0.166 3122 Planarity : 0.005 0.061 3696 Dihedral : 4.528 21.855 2870 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.36 % Allowed : 16.37 % Favored : 82.28 % 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: -1.18 (0.18), residues: 2541 helix: 0.97 (0.18), residues: 959 sheet: -1.01 (0.21), residues: 560 loop : -2.39 (0.22), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 132 HIS 0.006 0.001 HIS F 86 PHE 0.016 0.001 PHE A 368 TYR 0.013 0.001 TYR G 83 ARG 0.012 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 430 time to evaluate : 3.268 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9267 (m) cc_final: 0.8701 (t) REVERT: A 186 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8213 (ptp90) REVERT: A 189 ASP cc_start: 0.8404 (m-30) cc_final: 0.7908 (p0) REVERT: A 220 ILE cc_start: 0.9150 (mm) cc_final: 0.8898 (mm) REVERT: A 379 ASN cc_start: 0.7577 (t0) cc_final: 0.7232 (t0) REVERT: B 47 TYR cc_start: 0.5940 (m-80) cc_final: 0.4720 (m-80) REVERT: B 177 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7200 (mtt-85) REVERT: B 217 ASP cc_start: 0.7629 (m-30) cc_final: 0.7120 (m-30) REVERT: B 223 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7612 (ttp-110) REVERT: B 248 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 360 GLN cc_start: 0.7697 (tt0) cc_final: 0.7256 (tt0) REVERT: C 189 ASP cc_start: 0.8865 (m-30) cc_final: 0.8276 (p0) REVERT: C 325 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8348 (tmm-80) REVERT: C 359 TRP cc_start: 0.8041 (t60) cc_final: 0.7722 (t-100) REVERT: C 379 ASN cc_start: 0.8021 (t0) cc_final: 0.7721 (t0) REVERT: C 382 GLU cc_start: 0.8073 (tp30) cc_final: 0.7817 (tp30) REVERT: C 390 GLU cc_start: 0.8585 (pm20) cc_final: 0.8029 (pm20) REVERT: C 408 MET cc_start: 0.7965 (mtt) cc_final: 0.7612 (mtt) REVERT: D 80 GLU cc_start: 0.6952 (tt0) cc_final: 0.6581 (mt-10) REVERT: D 168 MET cc_start: 0.8033 (ttm) cc_final: 0.7782 (ttm) REVERT: D 189 ASP cc_start: 0.8346 (m-30) cc_final: 0.7872 (p0) REVERT: D 213 LYS cc_start: 0.8201 (tptp) cc_final: 0.7894 (tmtt) REVERT: D 248 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7804 (mm-30) REVERT: D 360 GLN cc_start: 0.7854 (tt0) cc_final: 0.7616 (tt0) REVERT: D 379 ASN cc_start: 0.7703 (t0) cc_final: 0.7418 (t0) REVERT: E 80 GLU cc_start: 0.7014 (tt0) cc_final: 0.6810 (mt-10) REVERT: E 92 SER cc_start: 0.8309 (m) cc_final: 0.7990 (t) REVERT: E 94 LYS cc_start: 0.8463 (tttp) cc_final: 0.8141 (tttt) REVERT: E 116 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7049 (mt-10) REVERT: E 165 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8245 (mmtp) REVERT: E 177 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7233 (mmt90) REVERT: E 189 ASP cc_start: 0.8419 (m-30) cc_final: 0.7584 (p0) REVERT: E 390 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: E 401 MET cc_start: 0.7560 (ttt) cc_final: 0.7325 (ttt) REVERT: F 73 ARG cc_start: 0.7342 (mmt180) cc_final: 0.6921 (mmt180) REVERT: F 80 GLU cc_start: 0.7696 (tt0) cc_final: 0.7272 (mt-10) REVERT: F 116 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6556 (mt-10) REVERT: F 134 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8298 (p) REVERT: F 162 GLU cc_start: 0.7863 (tp30) cc_final: 0.7321 (tp30) REVERT: F 177 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7270 (mtt-85) REVERT: F 234 CYS cc_start: 0.7605 (t) cc_final: 0.7297 (t) REVERT: G 47 TYR cc_start: 0.6117 (m-80) cc_final: 0.5173 (m-80) REVERT: G 98 ILE cc_start: 0.9019 (mm) cc_final: 0.8754 (mt) REVERT: G 177 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7606 (mmm-85) REVERT: G 189 ASP cc_start: 0.8832 (m-30) cc_final: 0.8195 (p0) REVERT: G 217 ASP cc_start: 0.8091 (m-30) cc_final: 0.7730 (m-30) REVERT: G 346 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7768 (mtp180) REVERT: G 413 ASN cc_start: 0.8070 (m110) cc_final: 0.7803 (m110) outliers start: 30 outliers final: 27 residues processed: 439 average time/residue: 0.8653 time to fit residues: 543.5363 Evaluate side-chains 447 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 418 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 356 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 332 ASN C 161 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN G 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21210 Z= 0.316 Angle : 0.554 6.268 28763 Z= 0.300 Chirality : 0.039 0.165 3122 Planarity : 0.005 0.064 3696 Dihedral : 4.870 24.924 2870 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 2.12 % Allowed : 17.18 % Favored : 80.70 % 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: -1.31 (0.18), residues: 2541 helix: 0.75 (0.18), residues: 959 sheet: -1.00 (0.23), residues: 525 loop : -2.36 (0.21), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 132 HIS 0.006 0.001 HIS E 70 PHE 0.021 0.002 PHE B 368 TYR 0.020 0.002 TYR G 83 ARG 0.009 0.001 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 435 time to evaluate : 3.281 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.8663 (m) cc_final: 0.8032 (t) REVERT: A 186 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8392 (ptp90) REVERT: A 189 ASP cc_start: 0.8396 (m-30) cc_final: 0.7864 (p0) REVERT: A 379 ASN cc_start: 0.7632 (t0) cc_final: 0.7343 (t0) REVERT: B 47 TYR cc_start: 0.5792 (m-80) cc_final: 0.5232 (m-80) REVERT: B 162 GLU cc_start: 0.7354 (tp30) cc_final: 0.7051 (tp30) REVERT: B 177 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7173 (mtt-85) REVERT: B 223 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7670 (ttp-110) REVERT: B 248 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7786 (mm-30) REVERT: B 277 SER cc_start: 0.8840 (p) cc_final: 0.8443 (m) REVERT: B 360 GLN cc_start: 0.7856 (tt0) cc_final: 0.7404 (tt0) REVERT: B 401 MET cc_start: 0.8357 (tpt) cc_final: 0.7357 (tpt) REVERT: C 145 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7788 (tppt) REVERT: C 189 ASP cc_start: 0.8924 (m-30) cc_final: 0.8364 (p0) REVERT: C 325 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8312 (tmm-80) REVERT: C 379 ASN cc_start: 0.8067 (t0) cc_final: 0.7745 (t0) REVERT: C 382 GLU cc_start: 0.8091 (tp30) cc_final: 0.7602 (tp30) REVERT: C 401 MET cc_start: 0.7809 (tpt) cc_final: 0.6388 (tpt) REVERT: C 408 MET cc_start: 0.7646 (mtt) cc_final: 0.7279 (mtt) REVERT: D 133 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7917 (mt-10) REVERT: D 168 MET cc_start: 0.8088 (ttm) cc_final: 0.7565 (ttm) REVERT: D 189 ASP cc_start: 0.8488 (m-30) cc_final: 0.8021 (p0) REVERT: D 213 LYS cc_start: 0.8155 (tptp) cc_final: 0.7872 (tmtt) REVERT: D 277 SER cc_start: 0.8231 (p) cc_final: 0.7831 (m) REVERT: D 360 GLN cc_start: 0.7982 (tt0) cc_final: 0.7717 (tt0) REVERT: D 379 ASN cc_start: 0.7754 (t0) cc_final: 0.7446 (t0) REVERT: E 47 TYR cc_start: 0.5438 (m-80) cc_final: 0.4796 (m-80) REVERT: E 80 GLU cc_start: 0.7010 (tt0) cc_final: 0.6732 (mt-10) REVERT: E 92 SER cc_start: 0.8452 (m) cc_final: 0.8184 (t) REVERT: E 94 LYS cc_start: 0.8477 (tttp) cc_final: 0.8156 (tttt) REVERT: E 165 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8287 (mmtp) REVERT: E 189 ASP cc_start: 0.8600 (m-30) cc_final: 0.7593 (p0) REVERT: E 401 MET cc_start: 0.7690 (ttt) cc_final: 0.7467 (ttt) REVERT: F 73 ARG cc_start: 0.7315 (mmt180) cc_final: 0.6881 (mmt180) REVERT: F 80 GLU cc_start: 0.7669 (tt0) cc_final: 0.7312 (mt-10) REVERT: F 177 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7233 (mtt-85) REVERT: F 218 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7987 (mtt90) REVERT: F 365 PHE cc_start: 0.7187 (t80) cc_final: 0.6779 (t80) REVERT: F 390 GLU cc_start: 0.8220 (pm20) cc_final: 0.7725 (pm20) REVERT: F 413 ASN cc_start: 0.8292 (m110) cc_final: 0.8015 (m110) REVERT: G 47 TYR cc_start: 0.6134 (m-80) cc_final: 0.5177 (m-80) REVERT: G 177 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7604 (mmm-85) REVERT: G 189 ASP cc_start: 0.8865 (m-30) cc_final: 0.8265 (p0) REVERT: G 217 ASP cc_start: 0.7852 (m-30) cc_final: 0.7618 (m-30) REVERT: G 413 ASN cc_start: 0.8179 (m110) cc_final: 0.7907 (m110) outliers start: 47 outliers final: 36 residues processed: 458 average time/residue: 0.8587 time to fit residues: 566.2216 Evaluate side-chains 458 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 422 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 TYR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 236 LYS Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 356 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 152 optimal weight: 0.0870 chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN F 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21210 Z= 0.192 Angle : 0.498 6.800 28763 Z= 0.265 Chirality : 0.037 0.164 3122 Planarity : 0.005 0.061 3696 Dihedral : 4.624 22.046 2870 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.67 % Allowed : 18.17 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.18), residues: 2541 helix: 1.01 (0.18), residues: 952 sheet: -0.82 (0.22), residues: 567 loop : -2.34 (0.22), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 132 HIS 0.005 0.001 HIS B 86 PHE 0.021 0.002 PHE F 208 TYR 0.015 0.001 TYR G 83 ARG 0.008 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 441 time to evaluate : 3.436 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9259 (m) cc_final: 0.8570 (t) REVERT: A 186 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8281 (ptp90) REVERT: A 189 ASP cc_start: 0.8527 (m-30) cc_final: 0.8009 (p0) REVERT: A 220 ILE cc_start: 0.9186 (mm) cc_final: 0.8956 (mm) REVERT: A 323 GLU cc_start: 0.8241 (pm20) cc_final: 0.7932 (pm20) REVERT: A 366 GLN cc_start: 0.7691 (tp40) cc_final: 0.7292 (tp-100) REVERT: A 379 ASN cc_start: 0.7605 (t0) cc_final: 0.7301 (t0) REVERT: B 47 TYR cc_start: 0.5624 (m-80) cc_final: 0.4454 (m-80) REVERT: B 177 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7179 (mtt-85) REVERT: B 223 ARG cc_start: 0.7929 (ttp-110) cc_final: 0.7719 (ttp-110) REVERT: B 248 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 277 SER cc_start: 0.8769 (p) cc_final: 0.8430 (m) REVERT: B 325 ARG cc_start: 0.8597 (tmm160) cc_final: 0.8369 (tmm160) REVERT: B 360 GLN cc_start: 0.7741 (tt0) cc_final: 0.7297 (tt0) REVERT: C 325 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8342 (tmm-80) REVERT: C 379 ASN cc_start: 0.8054 (t0) cc_final: 0.7722 (t0) REVERT: C 382 GLU cc_start: 0.8078 (tp30) cc_final: 0.7578 (tp30) REVERT: C 390 GLU cc_start: 0.8531 (pm20) cc_final: 0.7963 (pm20) REVERT: C 401 MET cc_start: 0.7839 (tpt) cc_final: 0.6420 (tpt) REVERT: C 408 MET cc_start: 0.7617 (mtt) cc_final: 0.7226 (mtt) REVERT: D 133 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7977 (mt-10) REVERT: D 168 MET cc_start: 0.8048 (ttm) cc_final: 0.7517 (ttm) REVERT: D 189 ASP cc_start: 0.8447 (m-30) cc_final: 0.7983 (p0) REVERT: D 213 LYS cc_start: 0.8168 (tptp) cc_final: 0.7868 (tmtt) REVERT: D 360 GLN cc_start: 0.7874 (tt0) cc_final: 0.7649 (tt0) REVERT: D 379 ASN cc_start: 0.7722 (t0) cc_final: 0.7426 (t0) REVERT: E 47 TYR cc_start: 0.5426 (m-80) cc_final: 0.4825 (m-80) REVERT: E 68 THR cc_start: 0.8612 (m) cc_final: 0.8351 (m) REVERT: E 80 GLU cc_start: 0.6966 (tt0) cc_final: 0.6705 (mt-10) REVERT: E 92 SER cc_start: 0.8373 (m) cc_final: 0.8047 (t) REVERT: E 94 LYS cc_start: 0.8451 (tttp) cc_final: 0.8154 (tttt) REVERT: E 165 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8267 (mmtp) REVERT: E 177 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7246 (mmt90) REVERT: E 189 ASP cc_start: 0.8552 (m-30) cc_final: 0.7544 (p0) REVERT: E 401 MET cc_start: 0.7429 (ttt) cc_final: 0.7158 (ttt) REVERT: F 73 ARG cc_start: 0.7273 (mmt180) cc_final: 0.6845 (mmt180) REVERT: F 80 GLU cc_start: 0.7656 (tt0) cc_final: 0.7276 (mt-10) REVERT: F 177 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7277 (mtt-85) REVERT: F 365 PHE cc_start: 0.7117 (t80) cc_final: 0.6680 (t80) REVERT: F 390 GLU cc_start: 0.8214 (pm20) cc_final: 0.7773 (pm20) REVERT: F 413 ASN cc_start: 0.8146 (m110) cc_final: 0.7869 (m110) REVERT: G 47 TYR cc_start: 0.6236 (m-80) cc_final: 0.5344 (m-80) REVERT: G 132 TRP cc_start: 0.7758 (t60) cc_final: 0.3775 (t60) REVERT: G 177 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7589 (mmm-85) REVERT: G 189 ASP cc_start: 0.8836 (m-30) cc_final: 0.8245 (p0) REVERT: G 217 ASP cc_start: 0.7793 (m-30) cc_final: 0.7437 (m-30) REVERT: G 223 ARG cc_start: 0.7845 (ttp-110) cc_final: 0.7471 (ttm110) REVERT: G 413 ASN cc_start: 0.8161 (m110) cc_final: 0.7896 (m110) outliers start: 37 outliers final: 31 residues processed: 458 average time/residue: 0.8709 time to fit residues: 580.8935 Evaluate side-chains 456 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 425 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 277 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 220 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21210 Z= 0.152 Angle : 0.480 7.469 28763 Z= 0.252 Chirality : 0.037 0.167 3122 Planarity : 0.004 0.064 3696 Dihedral : 4.411 20.879 2870 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 1.49 % Allowed : 18.54 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2541 helix: 1.25 (0.18), residues: 952 sheet: -0.70 (0.22), residues: 567 loop : -2.19 (0.22), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 214 HIS 0.005 0.001 HIS B 86 PHE 0.022 0.001 PHE F 208 TYR 0.020 0.001 TYR C 229 ARG 0.010 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 436 time to evaluate : 3.465 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9254 (m) cc_final: 0.8573 (t) REVERT: A 186 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8267 (ptp90) REVERT: A 189 ASP cc_start: 0.8422 (m-30) cc_final: 0.7898 (p0) REVERT: A 220 ILE cc_start: 0.9152 (mm) cc_final: 0.8937 (mm) REVERT: A 366 GLN cc_start: 0.7518 (tp40) cc_final: 0.7163 (tp-100) REVERT: A 379 ASN cc_start: 0.7599 (t0) cc_final: 0.7284 (t0) REVERT: B 47 TYR cc_start: 0.5789 (m-80) cc_final: 0.4686 (m-80) REVERT: B 177 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7078 (mtt-85) REVERT: B 223 ARG cc_start: 0.7984 (ttp-110) cc_final: 0.7679 (ttp-110) REVERT: B 248 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 277 SER cc_start: 0.8663 (p) cc_final: 0.8371 (m) REVERT: B 325 ARG cc_start: 0.8607 (tmm160) cc_final: 0.8356 (tmm160) REVERT: B 360 GLN cc_start: 0.7777 (tt0) cc_final: 0.7382 (tt0) REVERT: C 123 MET cc_start: 0.6719 (ptm) cc_final: 0.5941 (tmm) REVERT: C 132 TRP cc_start: 0.7558 (t60) cc_final: 0.4165 (t60) REVERT: C 240 ILE cc_start: 0.8749 (mm) cc_final: 0.8538 (mm) REVERT: C 325 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8361 (tmm-80) REVERT: C 379 ASN cc_start: 0.8053 (t0) cc_final: 0.7733 (t0) REVERT: C 382 GLU cc_start: 0.8076 (tp30) cc_final: 0.7815 (tp30) REVERT: C 390 GLU cc_start: 0.8520 (pm20) cc_final: 0.7948 (pm20) REVERT: C 401 MET cc_start: 0.7760 (tpt) cc_final: 0.6673 (tpt) REVERT: D 123 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5696 (ppp) REVERT: D 133 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7995 (mt-10) REVERT: D 168 MET cc_start: 0.8034 (ttm) cc_final: 0.7504 (ttm) REVERT: D 189 ASP cc_start: 0.8431 (m-30) cc_final: 0.7965 (p0) REVERT: D 213 LYS cc_start: 0.8218 (tptp) cc_final: 0.7938 (tmtt) REVERT: D 360 GLN cc_start: 0.7811 (tt0) cc_final: 0.7578 (tt0) REVERT: D 379 ASN cc_start: 0.7713 (t0) cc_final: 0.7453 (t0) REVERT: E 47 TYR cc_start: 0.5461 (m-80) cc_final: 0.4767 (m-80) REVERT: E 68 THR cc_start: 0.8595 (m) cc_final: 0.8312 (m) REVERT: E 80 GLU cc_start: 0.6902 (tt0) cc_final: 0.6665 (mt-10) REVERT: E 92 SER cc_start: 0.8316 (m) cc_final: 0.8034 (t) REVERT: E 94 LYS cc_start: 0.8429 (tttp) cc_final: 0.8117 (tttt) REVERT: E 122 GLN cc_start: 0.6691 (mt0) cc_final: 0.5792 (mt0) REVERT: E 165 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8254 (mmtp) REVERT: E 177 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7279 (mmt90) REVERT: E 189 ASP cc_start: 0.8534 (m-30) cc_final: 0.7563 (p0) REVERT: F 73 ARG cc_start: 0.7230 (mmt180) cc_final: 0.6793 (mmt180) REVERT: F 80 GLU cc_start: 0.7634 (tt0) cc_final: 0.7282 (mt-10) REVERT: F 177 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7280 (mtt-85) REVERT: F 234 CYS cc_start: 0.7575 (t) cc_final: 0.7234 (t) REVERT: F 365 PHE cc_start: 0.7059 (t80) cc_final: 0.6668 (t80) REVERT: F 390 GLU cc_start: 0.8297 (pm20) cc_final: 0.7885 (pm20) REVERT: F 413 ASN cc_start: 0.8134 (m110) cc_final: 0.7857 (m110) REVERT: G 47 TYR cc_start: 0.6138 (m-80) cc_final: 0.5252 (m-80) REVERT: G 132 TRP cc_start: 0.7719 (t60) cc_final: 0.3824 (t60) REVERT: G 177 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7581 (mmm-85) REVERT: G 189 ASP cc_start: 0.8831 (m-30) cc_final: 0.8223 (p0) REVERT: G 217 ASP cc_start: 0.7760 (m-30) cc_final: 0.7406 (m-30) REVERT: G 223 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7457 (ttm110) REVERT: G 413 ASN cc_start: 0.8179 (m110) cc_final: 0.7909 (m110) outliers start: 33 outliers final: 29 residues processed: 452 average time/residue: 0.8991 time to fit residues: 591.1637 Evaluate side-chains 451 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 421 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 210 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 226 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 225 optimal weight: 0.5980 chunk 148 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21210 Z= 0.141 Angle : 0.470 8.222 28763 Z= 0.245 Chirality : 0.037 0.167 3122 Planarity : 0.004 0.061 3696 Dihedral : 4.274 20.513 2870 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.13 % Allowed : 19.48 % Favored : 79.39 % 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: -0.64 (0.19), residues: 2541 helix: 1.35 (0.18), residues: 959 sheet: -0.58 (0.22), residues: 567 loop : -2.12 (0.22), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.003 0.001 HIS B 86 PHE 0.023 0.001 PHE F 208 TYR 0.018 0.001 TYR C 229 ARG 0.012 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 433 time to evaluate : 3.378 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9240 (m) cc_final: 0.8558 (t) REVERT: A 186 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8254 (ptp90) REVERT: A 189 ASP cc_start: 0.8419 (m-30) cc_final: 0.7890 (p0) REVERT: A 220 ILE cc_start: 0.9111 (mm) cc_final: 0.8886 (mm) REVERT: A 366 GLN cc_start: 0.7495 (tp40) cc_final: 0.7118 (tp-100) REVERT: A 379 ASN cc_start: 0.7592 (t0) cc_final: 0.7284 (t0) REVERT: B 47 TYR cc_start: 0.5744 (m-80) cc_final: 0.4653 (m-80) REVERT: B 177 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7088 (mtt-85) REVERT: B 223 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7666 (ttp-110) REVERT: B 248 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7872 (mm-30) REVERT: B 325 ARG cc_start: 0.8616 (tmm160) cc_final: 0.8379 (tmm160) REVERT: B 360 GLN cc_start: 0.7745 (tt0) cc_final: 0.7415 (tt0) REVERT: B 390 GLU cc_start: 0.8790 (pm20) cc_final: 0.8413 (pm20) REVERT: C 58 ARG cc_start: 0.8252 (mmt180) cc_final: 0.7948 (tpp80) REVERT: C 123 MET cc_start: 0.6664 (ptm) cc_final: 0.5974 (tmm) REVERT: C 132 TRP cc_start: 0.7524 (t60) cc_final: 0.4062 (t60) REVERT: C 213 LYS cc_start: 0.7818 (tmtt) cc_final: 0.7444 (tptp) REVERT: C 379 ASN cc_start: 0.8069 (t0) cc_final: 0.7768 (t0) REVERT: C 382 GLU cc_start: 0.8078 (tp30) cc_final: 0.7820 (tp30) REVERT: C 390 GLU cc_start: 0.8622 (pm20) cc_final: 0.8055 (pm20) REVERT: C 401 MET cc_start: 0.7864 (tpt) cc_final: 0.6461 (tpt) REVERT: D 123 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5588 (ppp) REVERT: D 133 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7993 (mt-10) REVERT: D 168 MET cc_start: 0.7973 (ttm) cc_final: 0.7548 (ttm) REVERT: D 189 ASP cc_start: 0.8422 (m-30) cc_final: 0.7956 (p0) REVERT: D 360 GLN cc_start: 0.7776 (tt0) cc_final: 0.7539 (tt0) REVERT: D 379 ASN cc_start: 0.7712 (t0) cc_final: 0.7451 (t0) REVERT: E 47 TYR cc_start: 0.5443 (m-80) cc_final: 0.4712 (m-80) REVERT: E 80 GLU cc_start: 0.6834 (tt0) cc_final: 0.6600 (mt-10) REVERT: E 92 SER cc_start: 0.8258 (m) cc_final: 0.7977 (t) REVERT: E 122 GLN cc_start: 0.6309 (mt0) cc_final: 0.5655 (mt0) REVERT: E 165 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8247 (mmtp) REVERT: E 177 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7281 (mmt90) REVERT: E 189 ASP cc_start: 0.8540 (m-30) cc_final: 0.7566 (p0) REVERT: F 31 MET cc_start: 0.0510 (mpp) cc_final: 0.0037 (tpt) REVERT: F 73 ARG cc_start: 0.7198 (mmt180) cc_final: 0.6766 (mmt180) REVERT: F 80 GLU cc_start: 0.7621 (tt0) cc_final: 0.7269 (mt-10) REVERT: F 177 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7280 (mtt-85) REVERT: F 234 CYS cc_start: 0.7510 (t) cc_final: 0.7213 (t) REVERT: F 365 PHE cc_start: 0.7126 (t80) cc_final: 0.6800 (t80) REVERT: F 390 GLU cc_start: 0.8288 (pm20) cc_final: 0.7888 (pm20) REVERT: F 413 ASN cc_start: 0.8042 (m110) cc_final: 0.7794 (m110) REVERT: G 47 TYR cc_start: 0.6257 (m-80) cc_final: 0.5350 (m-80) REVERT: G 132 TRP cc_start: 0.7711 (t60) cc_final: 0.3716 (t60) REVERT: G 177 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7586 (mmm-85) REVERT: G 189 ASP cc_start: 0.8828 (m-30) cc_final: 0.8206 (p0) REVERT: G 217 ASP cc_start: 0.7823 (m-30) cc_final: 0.7615 (m-30) REVERT: G 346 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7746 (mtm180) REVERT: G 413 ASN cc_start: 0.8176 (m110) cc_final: 0.7910 (m110) outliers start: 25 outliers final: 22 residues processed: 446 average time/residue: 0.8520 time to fit residues: 548.7836 Evaluate side-chains 453 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 430 time to evaluate : 4.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 134 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 251 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21210 Z= 0.146 Angle : 0.467 5.776 28763 Z= 0.245 Chirality : 0.037 0.168 3122 Planarity : 0.004 0.061 3696 Dihedral : 4.207 20.228 2870 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.04 % Allowed : 19.76 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 2541 helix: 1.40 (0.18), residues: 959 sheet: -0.52 (0.22), residues: 567 loop : -1.99 (0.23), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 214 HIS 0.003 0.001 HIS F 249 PHE 0.023 0.001 PHE F 208 TYR 0.020 0.001 TYR C 229 ARG 0.009 0.000 ARG A 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 433 time to evaluate : 3.388 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9255 (m) cc_final: 0.8560 (t) REVERT: A 186 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8250 (ptp90) REVERT: A 189 ASP cc_start: 0.8340 (m-30) cc_final: 0.7786 (p0) REVERT: A 220 ILE cc_start: 0.9100 (mm) cc_final: 0.8887 (mm) REVERT: A 366 GLN cc_start: 0.7608 (tp40) cc_final: 0.7302 (tp-100) REVERT: A 379 ASN cc_start: 0.7513 (t0) cc_final: 0.7169 (t0) REVERT: B 47 TYR cc_start: 0.5769 (m-80) cc_final: 0.4676 (m-80) REVERT: B 177 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7078 (mtt-85) REVERT: B 223 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7749 (ttp-110) REVERT: B 248 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 325 ARG cc_start: 0.8611 (tmm160) cc_final: 0.8387 (tmm160) REVERT: B 390 GLU cc_start: 0.8785 (pm20) cc_final: 0.8411 (pm20) REVERT: C 58 ARG cc_start: 0.8278 (mmt180) cc_final: 0.7983 (tpp80) REVERT: C 123 MET cc_start: 0.6713 (ptm) cc_final: 0.5950 (tmm) REVERT: C 132 TRP cc_start: 0.7536 (t60) cc_final: 0.4063 (t60) REVERT: C 213 LYS cc_start: 0.7943 (tmtt) cc_final: 0.7543 (tptp) REVERT: C 379 ASN cc_start: 0.8072 (t0) cc_final: 0.7774 (t0) REVERT: C 382 GLU cc_start: 0.8076 (tp30) cc_final: 0.7821 (tp30) REVERT: C 390 GLU cc_start: 0.8617 (pm20) cc_final: 0.8046 (pm20) REVERT: C 401 MET cc_start: 0.7879 (tpt) cc_final: 0.6469 (tpt) REVERT: D 56 ARG cc_start: 0.7049 (tmm160) cc_final: 0.6829 (ttp80) REVERT: D 168 MET cc_start: 0.7980 (ttm) cc_final: 0.7537 (ttm) REVERT: D 189 ASP cc_start: 0.8414 (m-30) cc_final: 0.7944 (p0) REVERT: D 360 GLN cc_start: 0.7752 (tt0) cc_final: 0.7527 (tt0) REVERT: D 379 ASN cc_start: 0.7717 (t0) cc_final: 0.7461 (t0) REVERT: E 47 TYR cc_start: 0.5454 (m-80) cc_final: 0.4711 (m-80) REVERT: E 80 GLU cc_start: 0.6822 (tt0) cc_final: 0.6531 (mt-10) REVERT: E 92 SER cc_start: 0.8288 (m) cc_final: 0.7999 (t) REVERT: E 165 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8246 (mmtp) REVERT: E 177 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7287 (mmt90) REVERT: E 189 ASP cc_start: 0.8541 (m-30) cc_final: 0.7573 (p0) REVERT: F 31 MET cc_start: 0.0493 (mpp) cc_final: 0.0029 (tpt) REVERT: F 80 GLU cc_start: 0.7601 (tt0) cc_final: 0.7179 (mt-10) REVERT: F 177 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7285 (mtt-85) REVERT: F 218 ARG cc_start: 0.8246 (mtm180) cc_final: 0.7979 (mtt90) REVERT: F 234 CYS cc_start: 0.7555 (t) cc_final: 0.7269 (t) REVERT: F 365 PHE cc_start: 0.7198 (t80) cc_final: 0.6915 (t80) REVERT: F 390 GLU cc_start: 0.8281 (pm20) cc_final: 0.7887 (pm20) REVERT: F 413 ASN cc_start: 0.8053 (m110) cc_final: 0.7800 (m110) REVERT: G 47 TYR cc_start: 0.6170 (m-80) cc_final: 0.5255 (m-80) REVERT: G 57 ASP cc_start: 0.7375 (m-30) cc_final: 0.6959 (m-30) REVERT: G 132 TRP cc_start: 0.7937 (t60) cc_final: 0.3937 (t60) REVERT: G 177 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7586 (mmm-85) REVERT: G 189 ASP cc_start: 0.8824 (m-30) cc_final: 0.8190 (p0) REVERT: G 217 ASP cc_start: 0.7755 (m-30) cc_final: 0.7417 (m-30) REVERT: G 413 ASN cc_start: 0.8229 (m110) cc_final: 0.7965 (m110) outliers start: 23 outliers final: 19 residues processed: 446 average time/residue: 0.8490 time to fit residues: 544.7352 Evaluate side-chains 447 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 428 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 175 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101270 restraints weight = 93771.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106428 restraints weight = 42394.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109871 restraints weight = 24958.976| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21210 Z= 0.159 Angle : 0.471 8.395 28763 Z= 0.246 Chirality : 0.037 0.170 3122 Planarity : 0.004 0.061 3696 Dihedral : 4.204 20.136 2870 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.08 % Allowed : 19.80 % Favored : 79.11 % 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: -0.50 (0.19), residues: 2541 helix: 1.39 (0.18), residues: 959 sheet: -0.51 (0.22), residues: 567 loop : -1.95 (0.23), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 214 HIS 0.004 0.001 HIS B 76 PHE 0.023 0.001 PHE F 208 TYR 0.021 0.001 TYR C 229 ARG 0.009 0.000 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9926.27 seconds wall clock time: 175 minutes 37.74 seconds (10537.74 seconds total)