Starting phenix.real_space_refine on Sat Aug 3 17:39:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/08_2024/8x16_37985.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/08_2024/8x16_37985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/08_2024/8x16_37985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/08_2024/8x16_37985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/08_2024/8x16_37985.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/08_2024/8x16_37985.cif" } resolution = 3.29 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= 0.006 sd= 0.071 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 I 1 10.91 5 S 68 5.16 5 C 5615 2.51 5 N 1468 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8751 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2268 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'Q8L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.13, per 1000 atoms: 0.59 Number of scatterers: 8751 At special positions: 0 Unit cell: (118.656, 92.288, 134.312, 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) I 1 52.95 S 68 16.00 O 1599 8.00 N 1468 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 166 " distance=2.06 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: 3.26 Conformation dependent library (CDL) restraints added in 1.6 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'R' and resid 9 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 47 through 64 removed outlier: 4.058A pdb=" N ILE R 51 " --> pdb=" O THR R 47 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 75 Processing helix chain 'R' and resid 79 through 114 removed outlier: 4.947A pdb=" N PHE R 85 " --> pdb=" O TYR R 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 143 Processing helix chain 'R' and resid 144 through 148 Processing helix chain 'R' and resid 181 through 186 Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 223 through 255 Proline residue: R 245 - end of helix Processing helix chain 'R' and resid 260 through 282 removed outlier: 3.840A pdb=" N ASN R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER R 275 " --> pdb=" O SER R 271 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET R 276 " --> pdb=" O HIS R 272 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 283 through 287 removed outlier: 3.745A pdb=" N ILE R 286 " --> pdb=" O ALA R 283 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS R 287 " --> pdb=" O TYR R 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 283 through 287' Processing helix chain 'R' and resid 288 through 299 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.538A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.751A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.007A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.746A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.662A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.651A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.889A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.747A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.599A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 77 through 78 removed outlier: 3.588A pdb=" N LEU R 164 " --> pdb=" O ILE R 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 191 removed outlier: 7.773A pdb=" N GLY A 183 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.611A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.129A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.058A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.674A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.613A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.068A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.648A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.781A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.909A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.770A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1194 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: 2.53 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 2836 1.37 - 1.55: 5994 1.55 - 1.74: 4 1.74 - 1.92: 101 1.92 - 2.11: 1 Bond restraints: 8936 Sorted by residual: bond pdb=" C5 Q8L R 401 " pdb=" O3 Q8L R 401 " ideal model delta sigma weight residual 1.419 1.667 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C1 Q8L R 401 " pdb=" C5 Q8L R 401 " ideal model delta sigma weight residual 1.530 1.286 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C2 Q8L R 401 " pdb=" O3 Q8L R 401 " ideal model delta sigma weight residual 1.432 1.299 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" N Q8L R 401 " pdb=" C3 Q8L R 401 " ideal model delta sigma weight residual 1.338 1.452 -0.114 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C10 Q8L R 401 " pdb=" N5 Q8L R 401 " ideal model delta sigma weight residual 1.347 1.454 -0.107 2.00e-02 2.50e+03 2.88e+01 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.70: 272 107.70 - 114.84: 5337 114.84 - 121.98: 4657 121.98 - 129.12: 1783 129.12 - 136.26: 68 Bond angle restraints: 12117 Sorted by residual: angle pdb=" C GLN R 167 " pdb=" N PHE R 168 " pdb=" CA PHE R 168 " ideal model delta sigma weight residual 121.54 136.26 -14.72 1.91e+00 2.74e-01 5.94e+01 angle pdb=" CA GLN R 167 " pdb=" C GLN R 167 " pdb=" O GLN R 167 " ideal model delta sigma weight residual 120.52 111.74 8.78 1.39e+00 5.18e-01 3.99e+01 angle pdb=" N SER R 82 " pdb=" CA SER R 82 " pdb=" C SER R 82 " ideal model delta sigma weight residual 111.02 101.47 9.55 1.52e+00 4.33e-01 3.95e+01 angle pdb=" N TYR R 81 " pdb=" CA TYR R 81 " pdb=" C TYR R 81 " ideal model delta sigma weight residual 112.97 106.71 6.26 1.06e+00 8.90e-01 3.49e+01 angle pdb=" N CYS R 166 " pdb=" CA CYS R 166 " pdb=" C CYS R 166 " ideal model delta sigma weight residual 108.73 116.17 -7.44 1.63e+00 3.76e-01 2.08e+01 ... (remaining 12112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5113 17.60 - 35.21: 140 35.21 - 52.81: 27 52.81 - 70.42: 2 70.42 - 88.02: 1 Dihedral angle restraints: 5283 sinusoidal: 2009 harmonic: 3274 Sorted by residual: dihedral pdb=" C SER R 82 " pdb=" N SER R 82 " pdb=" CA SER R 82 " pdb=" CB SER R 82 " ideal model delta harmonic sigma weight residual -122.60 -115.20 -7.40 0 2.50e+00 1.60e-01 8.76e+00 dihedral pdb=" CA SER R 242 " pdb=" C SER R 242 " pdb=" N TRP R 243 " pdb=" CA TRP R 243 " ideal model delta harmonic sigma weight residual -180.00 -166.08 -13.92 0 5.00e+00 4.00e-02 7.75e+00 dihedral pdb=" N GLN R 167 " pdb=" CA GLN R 167 " pdb=" CB GLN R 167 " pdb=" CG GLN R 167 " ideal model delta sinusoidal sigma weight residual -180.00 -136.96 -43.04 3 1.50e+01 4.44e-03 7.73e+00 ... (remaining 5280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1268 0.062 - 0.124: 125 0.124 - 0.186: 5 0.186 - 0.248: 1 0.248 - 0.310: 3 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CG LEU R 164 " pdb=" CB LEU R 164 " pdb=" CD1 LEU R 164 " pdb=" CD2 LEU R 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU R 164 " pdb=" N LEU R 164 " pdb=" C LEU R 164 " pdb=" CB LEU R 164 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA CYS R 166 " pdb=" N CYS R 166 " pdb=" C CYS R 166 " pdb=" CB CYS R 166 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1399 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 80 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C PHE R 80 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE R 80 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR R 81 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO H 236 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 164 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C LEU R 164 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU R 164 " 0.009 2.00e-02 2.50e+03 pdb=" N SER R 165 " 0.008 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.75: 966 2.75 - 3.31: 8970 3.31 - 3.86: 15001 3.86 - 4.41: 17966 4.41 - 4.96: 30929 Nonbonded interactions: 73832 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.203 3.040 nonbonded pdb=" CD1 PHE R 182 " pdb=" OG SER R 247 " model vdw 2.260 3.340 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.287 3.040 nonbonded pdb=" O VAL R 141 " pdb=" OH TYR R 176 " model vdw 2.292 3.040 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.313 3.120 ... (remaining 73827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 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 : 0.005 0.248 8936 Z= 0.308 Angle : 0.531 14.721 12117 Z= 0.302 Chirality : 0.041 0.310 1402 Planarity : 0.003 0.037 1507 Dihedral : 8.098 88.024 3168 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.92 % Rotamer: Outliers : 0.32 % Allowed : 4.80 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1108 helix: 0.28 (0.25), residues: 396 sheet: -0.61 (0.30), residues: 263 loop : -1.82 (0.25), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.002 0.000 HIS H 35 PHE 0.009 0.001 PHE A 189 TYR 0.006 0.001 TYR H 102 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 311 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.6825 (m) cc_final: 0.6518 (m) REVERT: R 175 ASP cc_start: 0.7181 (p0) cc_final: 0.6514 (p0) REVERT: A 302 TYR cc_start: 0.7277 (t80) cc_final: 0.6885 (t80) outliers start: 3 outliers final: 1 residues processed: 314 average time/residue: 0.2323 time to fit residues: 95.9407 Evaluate side-chains 188 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS B 16 ASN B 293 ASN C 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8936 Z= 0.256 Angle : 0.613 7.803 12117 Z= 0.316 Chirality : 0.044 0.196 1402 Planarity : 0.004 0.063 1507 Dihedral : 4.943 86.924 1242 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.09 % Allowed : 15.25 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1108 helix: 1.20 (0.27), residues: 395 sheet: -0.38 (0.30), residues: 266 loop : -1.54 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 243 HIS 0.004 0.001 HIS B 54 PHE 0.024 0.002 PHE H 68 TYR 0.017 0.002 TYR R 265 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 173 ARG cc_start: 0.7521 (mtp-110) cc_final: 0.7293 (mtm110) REVERT: R 190 LEU cc_start: 0.8206 (tt) cc_final: 0.7673 (tt) REVERT: H 244 LYS cc_start: 0.7014 (ttmm) cc_final: 0.6809 (tttp) outliers start: 29 outliers final: 12 residues processed: 231 average time/residue: 0.2045 time to fit residues: 65.2903 Evaluate side-chains 185 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8936 Z= 0.183 Angle : 0.559 7.370 12117 Z= 0.285 Chirality : 0.042 0.207 1402 Planarity : 0.003 0.066 1507 Dihedral : 4.735 89.375 1240 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.77 % Allowed : 16.63 % Favored : 80.60 % 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: -0.03 (0.25), residues: 1108 helix: 1.48 (0.27), residues: 395 sheet: -0.18 (0.31), residues: 264 loop : -1.27 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.012 0.001 HIS R 124 PHE 0.023 0.001 PHE A 191 TYR 0.011 0.001 TYR A 296 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 MET cc_start: 0.7371 (mmm) cc_final: 0.7164 (mmm) REVERT: B 105 TYR cc_start: 0.8458 (t80) cc_final: 0.8105 (t80) REVERT: H 30 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.8058 (m) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 0.2084 time to fit residues: 56.0691 Evaluate side-chains 179 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 0.1980 chunk 51 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.0270 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.0170 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 0.0470 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.1574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS A 52 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8936 Z= 0.140 Angle : 0.537 8.871 12117 Z= 0.273 Chirality : 0.041 0.197 1402 Planarity : 0.003 0.061 1507 Dihedral : 4.518 89.305 1240 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.77 % Allowed : 18.44 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1108 helix: 1.61 (0.27), residues: 392 sheet: -0.11 (0.31), residues: 268 loop : -1.07 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 47 HIS 0.002 0.000 HIS R 124 PHE 0.028 0.001 PHE R 182 TYR 0.019 0.001 TYR A 230 ARG 0.009 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.7444 (m) cc_final: 0.7016 (m) REVERT: R 73 SER cc_start: 0.8725 (p) cc_final: 0.8400 (t) REVERT: R 102 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7822 (tm) REVERT: R 232 LEU cc_start: 0.7170 (mp) cc_final: 0.6666 (tt) outliers start: 26 outliers final: 13 residues processed: 194 average time/residue: 0.1975 time to fit residues: 52.6402 Evaluate side-chains 175 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 0.0470 overall best weight: 2.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8936 Z= 0.332 Angle : 0.707 11.432 12117 Z= 0.359 Chirality : 0.046 0.249 1402 Planarity : 0.005 0.081 1507 Dihedral : 5.258 87.913 1240 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.37 % Allowed : 17.70 % Favored : 77.93 % 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: 0.06 (0.25), residues: 1108 helix: 1.46 (0.27), residues: 394 sheet: -0.25 (0.31), residues: 280 loop : -1.03 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 243 HIS 0.011 0.002 HIS R 124 PHE 0.030 0.002 PHE R 182 TYR 0.017 0.002 TYR H 50 ARG 0.014 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.7524 (m) cc_final: 0.7182 (m) REVERT: R 232 LEU cc_start: 0.7253 (mp) cc_final: 0.6756 (tt) REVERT: B 142 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6556 (m90) REVERT: B 223 THR cc_start: 0.7837 (p) cc_final: 0.7583 (p) outliers start: 41 outliers final: 22 residues processed: 215 average time/residue: 0.2097 time to fit residues: 61.8040 Evaluate side-chains 188 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN B 237 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8936 Z= 0.257 Angle : 0.650 11.195 12117 Z= 0.325 Chirality : 0.044 0.174 1402 Planarity : 0.004 0.074 1507 Dihedral : 4.976 78.744 1240 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.58 % Allowed : 19.19 % Favored : 76.23 % 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: 0.16 (0.25), residues: 1108 helix: 1.48 (0.27), residues: 397 sheet: -0.14 (0.31), residues: 280 loop : -0.97 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 47 HIS 0.006 0.001 HIS B 54 PHE 0.047 0.002 PHE R 255 TYR 0.038 0.002 TYR R 265 ARG 0.005 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 150 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.5983 (t0) REVERT: R 232 LEU cc_start: 0.7288 (mp) cc_final: 0.6784 (tt) REVERT: A 247 MET cc_start: 0.6400 (ptt) cc_final: 0.6113 (ptm) REVERT: B 142 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7055 (m90) REVERT: H 62 ASP cc_start: 0.7052 (m-30) cc_final: 0.6741 (m-30) outliers start: 43 outliers final: 31 residues processed: 190 average time/residue: 0.1681 time to fit residues: 46.2592 Evaluate side-chains 183 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN B 237 ASN B 239 ASN B 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.7376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8936 Z= 0.175 Angle : 0.615 13.509 12117 Z= 0.302 Chirality : 0.043 0.171 1402 Planarity : 0.004 0.064 1507 Dihedral : 4.695 76.401 1240 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.73 % Allowed : 20.15 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1108 helix: 1.58 (0.27), residues: 397 sheet: -0.00 (0.31), residues: 268 loop : -0.92 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP H 47 HIS 0.003 0.001 HIS R 79 PHE 0.031 0.002 PHE R 182 TYR 0.026 0.001 TYR R 265 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 150 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.5815 (t0) REVERT: R 232 LEU cc_start: 0.7370 (mp) cc_final: 0.6755 (tt) REVERT: R 256 ASN cc_start: 0.8343 (m-40) cc_final: 0.8037 (m-40) REVERT: R 265 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 247 MET cc_start: 0.6345 (ptt) cc_final: 0.6116 (ptm) REVERT: H 62 ASP cc_start: 0.7032 (m-30) cc_final: 0.6722 (m-30) REVERT: H 233 LEU cc_start: 0.8365 (tp) cc_final: 0.8155 (tp) outliers start: 35 outliers final: 25 residues processed: 184 average time/residue: 0.1715 time to fit residues: 45.4874 Evaluate side-chains 179 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8936 Z= 0.222 Angle : 0.645 14.306 12117 Z= 0.319 Chirality : 0.043 0.163 1402 Planarity : 0.004 0.052 1507 Dihedral : 4.722 74.762 1240 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.73 % Allowed : 20.04 % Favored : 76.23 % 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: 0.38 (0.26), residues: 1108 helix: 1.72 (0.27), residues: 397 sheet: 0.03 (0.32), residues: 254 loop : -0.91 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP H 47 HIS 0.003 0.001 HIS H 167 PHE 0.052 0.002 PHE R 255 TYR 0.026 0.001 TYR R 265 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 150 ASN cc_start: 0.6351 (OUTLIER) cc_final: 0.5757 (t0) REVERT: R 172 MET cc_start: 0.8269 (ptp) cc_final: 0.7895 (mtt) REVERT: R 232 LEU cc_start: 0.7394 (mp) cc_final: 0.6784 (tt) REVERT: R 256 ASN cc_start: 0.8438 (m-40) cc_final: 0.8136 (m110) REVERT: R 265 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7386 (t80) REVERT: A 247 MET cc_start: 0.6537 (ptt) cc_final: 0.6296 (ptm) REVERT: H 62 ASP cc_start: 0.7131 (m-30) cc_final: 0.6789 (m-30) REVERT: H 232 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7462 (t70) outliers start: 35 outliers final: 28 residues processed: 175 average time/residue: 0.1820 time to fit residues: 45.7323 Evaluate side-chains 177 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 0.0970 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8936 Z= 0.231 Angle : 0.644 14.006 12117 Z= 0.321 Chirality : 0.044 0.148 1402 Planarity : 0.003 0.049 1507 Dihedral : 4.697 71.993 1240 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.73 % Allowed : 20.79 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1108 helix: 1.69 (0.28), residues: 396 sheet: -0.00 (0.32), residues: 254 loop : -0.91 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP H 47 HIS 0.004 0.001 HIS H 167 PHE 0.045 0.002 PHE R 255 TYR 0.026 0.001 TYR R 265 ARG 0.008 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 150 ASN cc_start: 0.6620 (OUTLIER) cc_final: 0.5810 (t0) REVERT: R 232 LEU cc_start: 0.7393 (mp) cc_final: 0.6830 (tt) REVERT: R 265 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7758 (t80) REVERT: A 247 MET cc_start: 0.6620 (ptt) cc_final: 0.6396 (ptm) REVERT: H 62 ASP cc_start: 0.7076 (m-30) cc_final: 0.6739 (m-30) REVERT: H 232 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7324 (t70) outliers start: 35 outliers final: 31 residues processed: 174 average time/residue: 0.1914 time to fit residues: 47.5270 Evaluate side-chains 181 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 232 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.8154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8936 Z= 0.195 Angle : 0.666 13.775 12117 Z= 0.329 Chirality : 0.044 0.173 1402 Planarity : 0.003 0.044 1507 Dihedral : 4.580 70.443 1240 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.62 % Allowed : 22.07 % Favored : 74.31 % 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: 0.34 (0.26), residues: 1108 helix: 1.76 (0.27), residues: 393 sheet: -0.01 (0.32), residues: 256 loop : -0.97 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP R 185 HIS 0.003 0.001 HIS H 167 PHE 0.050 0.002 PHE R 255 TYR 0.025 0.001 TYR A 296 ARG 0.004 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 150 ASN cc_start: 0.6426 (OUTLIER) cc_final: 0.5858 (t0) REVERT: R 232 LEU cc_start: 0.7384 (mp) cc_final: 0.6836 (tt) REVERT: R 265 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7795 (t80) REVERT: B 181 THR cc_start: 0.7852 (p) cc_final: 0.7487 (p) REVERT: H 62 ASP cc_start: 0.6972 (m-30) cc_final: 0.6651 (m-30) REVERT: H 232 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7340 (t70) outliers start: 34 outliers final: 27 residues processed: 174 average time/residue: 0.1808 time to fit residues: 45.0812 Evaluate side-chains 178 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 232 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.0470 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.176438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132040 restraints weight = 12958.426| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.99 r_work: 0.3610 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.8224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8936 Z= 0.175 Angle : 0.649 13.626 12117 Z= 0.319 Chirality : 0.044 0.172 1402 Planarity : 0.003 0.042 1507 Dihedral : 4.487 69.178 1240 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.30 % Allowed : 21.96 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1108 helix: 1.78 (0.28), residues: 393 sheet: 0.05 (0.32), residues: 256 loop : -0.95 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 47 HIS 0.002 0.001 HIS B 225 PHE 0.051 0.002 PHE R 255 TYR 0.024 0.001 TYR A 296 ARG 0.004 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.88 seconds wall clock time: 42 minutes 44.75 seconds (2564.75 seconds total)