Starting phenix.real_space_refine on Fri Jul 19 17:54:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/07_2024/8x16_37985.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/07_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_37985/07_2024/8x16_37985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/07_2024/8x16_37985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/07_2024/8x16_37985.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/07_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.26, per 1000 atoms: 0.60 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: 3.33 Conformation dependent library (CDL) restraints added in 1.4 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: 1.06 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: 2.79 Time building geometry restraints manager: 3.65 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 2.440 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 2.440 nonbonded pdb=" O VAL R 141 " pdb=" OH TYR R 176 " model vdw 2.292 2.440 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.313 2.520 ... (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 ========== 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: 1.120 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.240 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- 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 : 0.869 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: 0.2341 time to fit residues: 96.5907 Evaluate side-chains 188 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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: 5.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 7.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 268 ASN B 293 ASN C 24 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8936 Z= 0.188 Angle : 0.538 7.306 12117 Z= 0.275 Chirality : 0.041 0.182 1402 Planarity : 0.004 0.070 1507 Dihedral : 4.720 86.938 1242 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.03 % Allowed : 16.31 % 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: -0.29 (0.25), residues: 1108 helix: 1.38 (0.27), residues: 393 sheet: -0.40 (0.30), residues: 276 loop : -1.49 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS R 158 PHE 0.021 0.002 PHE A 191 TYR 0.012 0.001 TYR H 60 ARG 0.007 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 217 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 0.975 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: 0.7113 (m) cc_final: 0.6894 (m) REVERT: R 173 ARG cc_start: 0.7253 (mtp-110) cc_final: 0.7016 (mtm110) REVERT: A 276 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7147 (tm-30) outliers start: 19 outliers final: 11 residues processed: 208 average time/residue: 0.2086 time to fit residues: 59.7902 Evaluate side-chains 176 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 ASP 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 276 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.0870 overall best weight: 1.3764 ------------------------------------------------------------------------------- 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** B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8936 Z= 0.243 Angle : 0.574 8.201 12117 Z= 0.300 Chirality : 0.042 0.169 1402 Planarity : 0.004 0.059 1507 Dihedral : 4.662 87.792 1240 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.73 % Allowed : 15.67 % 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: 0.02 (0.25), residues: 1108 helix: 1.51 (0.27), residues: 395 sheet: -0.23 (0.31), residues: 277 loop : -1.19 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.033 0.002 HIS R 124 PHE 0.019 0.002 PHE R 182 TYR 0.012 0.001 TYR H 190 ARG 0.005 0.001 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 228 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.7379 (m) cc_final: 0.7161 (m) REVERT: R 102 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7794 (tm) REVERT: R 173 ARG cc_start: 0.7443 (mtp-110) cc_final: 0.7127 (mtp-110) REVERT: H 30 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7926 (m) outliers start: 35 outliers final: 23 residues processed: 215 average time/residue: 0.2041 time to fit residues: 60.5820 Evaluate side-chains 194 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 185 VAL 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 332 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 0.0060 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.0180 ------------------------------------------------------------------------------- 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 322 HIS B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8936 Z= 0.304 Angle : 0.634 7.163 12117 Z= 0.329 Chirality : 0.045 0.184 1402 Planarity : 0.004 0.055 1507 Dihedral : 5.130 89.539 1240 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.37 % Allowed : 16.74 % Favored : 78.89 % 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: 0.05 (0.25), residues: 1108 helix: 1.51 (0.27), residues: 396 sheet: -0.17 (0.31), residues: 264 loop : -1.15 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS H 167 PHE 0.032 0.002 PHE R 182 TYR 0.020 0.002 TYR A 230 ARG 0.008 0.001 ARG A 205 *********************** 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 234 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.7543 (m) cc_final: 0.7182 (m) REVERT: R 173 ARG cc_start: 0.7528 (mtp-110) cc_final: 0.7209 (mtm110) REVERT: R 232 LEU cc_start: 0.7164 (mp) cc_final: 0.6666 (tt) REVERT: A 255 ASN cc_start: 0.7831 (m-40) cc_final: 0.7472 (m-40) REVERT: A 278 ILE cc_start: 0.5663 (OUTLIER) cc_final: 0.5415 (mm) REVERT: H 30 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8208 (m) outliers start: 41 outliers final: 24 residues processed: 216 average time/residue: 0.2040 time to fit residues: 60.1746 Evaluate side-chains 193 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 124 HIS Chi-restraints excluded: chain R residue 127 ILE 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 26 ASP Chi-restraints excluded: chain A residue 52 GLN 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 278 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL 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 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.0370 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- 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 A 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8936 Z= 0.229 Angle : 0.592 8.484 12117 Z= 0.298 Chirality : 0.043 0.147 1402 Planarity : 0.003 0.044 1507 Dihedral : 4.815 80.917 1240 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.73 % Allowed : 20.36 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1108 helix: 1.67 (0.27), residues: 396 sheet: -0.27 (0.30), residues: 280 loop : -1.04 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 47 HIS 0.007 0.001 HIS R 124 PHE 0.032 0.002 PHE R 182 TYR 0.020 0.001 TYR R 15 ARG 0.005 0.000 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 213 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 232 LEU cc_start: 0.7153 (mp) cc_final: 0.6670 (tt) REVERT: A 255 ASN cc_start: 0.7834 (m-40) cc_final: 0.7264 (m-40) REVERT: A 278 ILE cc_start: 0.5770 (OUTLIER) cc_final: 0.5475 (mm) REVERT: B 142 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6666 (m90) REVERT: B 169 TRP cc_start: 0.7970 (m100) cc_final: 0.7718 (m100) REVERT: H 30 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8345 (m) REVERT: H 183 GLN cc_start: 0.5732 (pt0) cc_final: 0.5523 (pt0) outliers start: 35 outliers final: 20 residues processed: 195 average time/residue: 0.2032 time to fit residues: 55.1955 Evaluate side-chains 189 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 278 ILE 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 142 HIS 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 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 255 ASN B 237 ASN B 239 ASN B 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.7326 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= 0.292 Angle : 0.634 8.935 12117 Z= 0.322 Chirality : 0.044 0.156 1402 Planarity : 0.004 0.043 1507 Dihedral : 4.954 78.683 1240 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.26 % Allowed : 20.04 % Favored : 75.69 % 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: 0.09 (0.25), residues: 1108 helix: 1.51 (0.27), residues: 394 sheet: -0.19 (0.31), residues: 263 loop : -1.07 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 47 HIS 0.004 0.001 HIS A 195 PHE 0.045 0.002 PHE R 255 TYR 0.019 0.002 TYR R 15 ARG 0.010 0.001 ARG H 87 *********************** 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: 40 poor density : 168 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 124 HIS cc_start: 0.6220 (OUTLIER) cc_final: 0.5422 (t70) REVERT: R 232 LEU cc_start: 0.7212 (mp) cc_final: 0.6723 (tt) REVERT: B 142 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7131 (m90) REVERT: B 220 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6947 (mm-40) REVERT: B 293 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7844 (p0) outliers start: 40 outliers final: 24 residues processed: 192 average time/residue: 0.2000 time to fit residues: 53.1472 Evaluate side-chains 185 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR 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 293 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 255 ASN A 331 ASN B 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.7554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8936 Z= 0.193 Angle : 0.592 11.728 12117 Z= 0.296 Chirality : 0.042 0.147 1402 Planarity : 0.003 0.032 1507 Dihedral : 4.771 76.975 1240 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.20 % Allowed : 21.43 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1108 helix: 1.60 (0.27), residues: 390 sheet: -0.09 (0.31), residues: 269 loop : -0.96 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 47 HIS 0.003 0.001 HIS R 124 PHE 0.037 0.002 PHE R 168 TYR 0.012 0.001 TYR B 105 ARG 0.007 0.001 ARG H 87 *********************** 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 194 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 124 HIS cc_start: 0.6122 (OUTLIER) cc_final: 0.5509 (t70) REVERT: R 232 LEU cc_start: 0.7209 (mp) cc_final: 0.6707 (tt) REVERT: R 256 ASN cc_start: 0.8466 (m-40) cc_final: 0.8184 (m-40) REVERT: A 255 ASN cc_start: 0.7580 (m110) cc_final: 0.7326 (m-40) REVERT: B 142 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7343 (m90) REVERT: B 220 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6915 (mm-40) REVERT: B 293 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7789 (p0) REVERT: H 62 ASP cc_start: 0.7295 (m-30) cc_final: 0.7028 (m-30) outliers start: 30 outliers final: 20 residues processed: 183 average time/residue: 0.1957 time to fit residues: 50.1809 Evaluate side-chains 182 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 124 HIS Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU 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 185 VAL Chi-restraints excluded: chain A residue 190 THR 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 101 MET 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 293 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 194 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- 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 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.7736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8936 Z= 0.213 Angle : 0.590 11.190 12117 Z= 0.295 Chirality : 0.042 0.172 1402 Planarity : 0.003 0.030 1507 Dihedral : 4.727 75.471 1240 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.52 % Allowed : 21.11 % Favored : 75.37 % 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 (0.26), residues: 1108 helix: 1.68 (0.27), residues: 389 sheet: -0.06 (0.32), residues: 269 loop : -0.93 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 47 HIS 0.004 0.001 HIS A 195 PHE 0.047 0.002 PHE R 255 TYR 0.015 0.001 TYR A 296 ARG 0.007 0.001 ARG A 24 *********************** 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 196 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 124 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.5586 (t70) REVERT: R 232 LEU cc_start: 0.7299 (mp) cc_final: 0.6734 (tt) REVERT: R 256 ASN cc_start: 0.8560 (m-40) cc_final: 0.8256 (m-40) REVERT: A 255 ASN cc_start: 0.7772 (m110) cc_final: 0.7499 (m-40) REVERT: B 142 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7549 (m90) REVERT: B 220 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6945 (mm-40) REVERT: B 293 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7708 (p0) REVERT: H 62 ASP cc_start: 0.7326 (m-30) cc_final: 0.7037 (m-30) outliers start: 33 outliers final: 25 residues processed: 180 average time/residue: 0.1895 time to fit residues: 47.9526 Evaluate side-chains 184 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 149 TRP 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 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR 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 101 MET 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 293 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.0030 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.7816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8936 Z= 0.180 Angle : 0.581 10.412 12117 Z= 0.289 Chirality : 0.042 0.171 1402 Planarity : 0.003 0.032 1507 Dihedral : 4.624 74.476 1240 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.20 % Allowed : 21.54 % Favored : 75.27 % 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: 0.37 (0.26), residues: 1108 helix: 1.71 (0.27), residues: 390 sheet: 0.03 (0.32), residues: 265 loop : -0.90 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.002 0.001 HIS R 158 PHE 0.048 0.002 PHE R 255 TYR 0.009 0.001 TYR B 105 ARG 0.008 0.001 ARG A 24 *********************** 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 190 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 124 HIS cc_start: 0.6147 (OUTLIER) cc_final: 0.5527 (t70) REVERT: R 232 LEU cc_start: 0.7310 (mp) cc_final: 0.6758 (tt) REVERT: A 255 ASN cc_start: 0.7781 (m110) cc_final: 0.7497 (m-40) REVERT: B 293 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7733 (p0) REVERT: H 62 ASP cc_start: 0.7297 (m-30) cc_final: 0.6999 (m-30) outliers start: 30 outliers final: 24 residues processed: 176 average time/residue: 0.1950 time to fit residues: 49.0320 Evaluate side-chains 182 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 149 TRP 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 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 190 THR 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 101 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.0570 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8936 Z= 0.179 Angle : 0.584 10.350 12117 Z= 0.293 Chirality : 0.042 0.215 1402 Planarity : 0.003 0.030 1507 Dihedral : 4.592 74.225 1240 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.09 % Allowed : 22.07 % Favored : 74.84 % 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: 0.45 (0.26), residues: 1108 helix: 1.77 (0.27), residues: 390 sheet: 0.17 (0.33), residues: 259 loop : -0.89 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 185 HIS 0.011 0.001 HIS B 142 PHE 0.048 0.002 PHE R 255 TYR 0.017 0.001 TYR A 296 ARG 0.007 0.000 ARG A 24 ********************** 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 184 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 172 MET cc_start: 0.8333 (mtm) cc_final: 0.7878 (mpp) REVERT: R 232 LEU cc_start: 0.7331 (mp) cc_final: 0.6788 (tt) REVERT: R 256 ASN cc_start: 0.8647 (m-40) cc_final: 0.8282 (m-40) REVERT: A 255 ASN cc_start: 0.7740 (m110) cc_final: 0.7469 (m-40) REVERT: B 293 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7788 (p0) REVERT: H 62 ASP cc_start: 0.7317 (m-30) cc_final: 0.7002 (m-30) outliers start: 29 outliers final: 26 residues processed: 170 average time/residue: 0.1847 time to fit residues: 44.7865 Evaluate side-chains 178 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 149 TRP 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 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 190 THR 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 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 87 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.0670 chunk 63 optimal weight: 4.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS B 239 ASN B 293 ASN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.177445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133678 restraints weight = 13015.756| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.96 r_work: 0.3642 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.7915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8936 Z= 0.159 Angle : 0.594 13.976 12117 Z= 0.293 Chirality : 0.042 0.226 1402 Planarity : 0.003 0.030 1507 Dihedral : 4.452 72.431 1240 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.45 % Allowed : 23.13 % Favored : 74.41 % 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: 0.58 (0.26), residues: 1108 helix: 1.93 (0.27), residues: 390 sheet: 0.32 (0.33), residues: 253 loop : -0.91 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 185 HIS 0.008 0.001 HIS B 142 PHE 0.049 0.002 PHE R 255 TYR 0.013 0.001 TYR R 15 ARG 0.007 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2401.39 seconds wall clock time: 43 minutes 23.51 seconds (2603.51 seconds total)