Starting phenix.real_space_refine on Fri Jul 19 18:57:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/07_2024/8w8r_37357_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/07_2024/8w8r_37357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/07_2024/8w8r_37357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/07_2024/8w8r_37357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/07_2024/8w8r_37357_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8r_37357/07_2024/8w8r_37357_neut.cif" } resolution = 3.3 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5759 2.51 5 N 1552 2.21 5 O 1644 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9018 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1955 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2572 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2223 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1782 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'U7D': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.31, per 1000 atoms: 0.59 Number of scatterers: 9018 At special positions: 0 Unit cell: (125.8, 123.25, 96.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 F 6 9.00 O 1644 8.00 N 1552 7.00 C 5759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 4.61 Conformation dependent library (CDL) restraints added in 1.6 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 35.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 25 through 49 removed outlier: 3.906A pdb=" N ALA A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 72 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.842A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 249' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.906A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.585A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.803A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.621A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 29 through 59 removed outlier: 3.817A pdb=" N VAL R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE R 40 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 41 " --> pdb=" O VAL R 37 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 93 removed outlier: 3.994A pdb=" N PHE R 69 " --> pdb=" O VAL R 65 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN R 80 " --> pdb=" O THR R 76 " (cutoff:3.500A) Proline residue: R 86 - end of helix removed outlier: 3.869A pdb=" N SER R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 134 removed outlier: 3.807A pdb=" N VAL R 108 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 164 Processing helix chain 'R' and resid 165 through 168 Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 189 through 201 Processing helix chain 'R' and resid 201 through 228 removed outlier: 4.156A pdb=" N VAL R 214 " --> pdb=" O ALA R 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL R 215 " --> pdb=" O CYS R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 397 through 422 removed outlier: 4.031A pdb=" N ILE R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Proline residue: R 414 - end of helix Processing helix chain 'R' and resid 432 through 445 removed outlier: 3.731A pdb=" N PHE R 444 " --> pdb=" O ILE R 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 455 Proline residue: R 451 - end of helix Processing helix chain 'R' and resid 458 through 473 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.542A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.861A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.811A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing helix chain 'Y' and resid 10 through 22 removed outlier: 3.796A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.542A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 223 removed outlier: 6.439A pdb=" N HIS A 51 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE A 232 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 53 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL A 234 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N LEU A 55 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG A 52 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE A 255 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 54 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 257 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 56 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ASP A 259 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.875A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.732A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.524A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.552A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.050A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.693A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.646A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 174 removed outlier: 4.407A pdb=" N GLN R 172 " --> pdb=" O ILE R 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.648A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.557A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.866A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1167 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: 2.46 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1461 1.32 - 1.45: 2593 1.45 - 1.57: 5084 1.57 - 1.70: 2 1.70 - 1.83: 79 Bond restraints: 9219 Sorted by residual: bond pdb=" C07 U7D R 602 " pdb=" N02 U7D R 602 " ideal model delta sigma weight residual 1.353 1.453 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C07 U7D R 601 " pdb=" N02 U7D R 601 " ideal model delta sigma weight residual 1.353 1.453 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C07 U7D R 602 " pdb=" N03 U7D R 602 " ideal model delta sigma weight residual 1.359 1.454 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" N LEU B 308 " pdb=" CA LEU B 308 " ideal model delta sigma weight residual 1.455 1.516 -0.061 1.32e-02 5.74e+03 2.14e+01 bond pdb=" C07 U7D R 601 " pdb=" N03 U7D R 601 " ideal model delta sigma weight residual 1.359 1.451 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 9214 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.32: 288 107.32 - 114.15: 5224 114.15 - 120.99: 4183 120.99 - 127.82: 2733 127.82 - 134.66: 85 Bond angle restraints: 12513 Sorted by residual: angle pdb=" N PRO R 165 " pdb=" CA PRO R 165 " pdb=" C PRO R 165 " ideal model delta sigma weight residual 110.70 119.95 -9.25 1.22e+00 6.72e-01 5.75e+01 angle pdb=" CA ILE B 232 " pdb=" C ILE B 232 " pdb=" O ILE B 232 " ideal model delta sigma weight residual 120.96 116.19 4.77 8.40e-01 1.42e+00 3.22e+01 angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 107.73 114.61 -6.88 1.34e+00 5.57e-01 2.63e+01 angle pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" O GLY B 310 " ideal model delta sigma weight residual 119.01 124.56 -5.55 1.11e+00 8.12e-01 2.50e+01 angle pdb=" N THR R 105 " pdb=" CA THR R 105 " pdb=" C THR R 105 " ideal model delta sigma weight residual 113.50 107.50 6.00 1.23e+00 6.61e-01 2.38e+01 ... (remaining 12508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4677 17.55 - 35.11: 588 35.11 - 52.66: 147 52.66 - 70.22: 31 70.22 - 87.77: 9 Dihedral angle restraints: 5452 sinusoidal: 2125 harmonic: 3327 Sorted by residual: dihedral pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta harmonic sigma weight residual 122.80 113.13 9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual -86.00 -117.74 31.74 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1180 0.067 - 0.134: 189 0.134 - 0.200: 32 0.200 - 0.267: 12 0.267 - 0.334: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA LEU B 190 " pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CB LEU B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1412 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 307 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C VAL B 307 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL B 307 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU B 308 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO S 236 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C PRO S 236 " 0.067 2.00e-02 2.50e+03 pdb=" O PRO S 236 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU S 237 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 234 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C PHE B 234 " -0.055 2.00e-02 2.50e+03 pdb=" O PHE B 234 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE B 235 " 0.019 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1382 2.76 - 3.30: 7813 3.30 - 3.83: 13690 3.83 - 4.37: 15924 4.37 - 4.90: 29526 Nonbonded interactions: 68335 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.227 2.440 nonbonded pdb=" O THR S 144 " pdb=" OG1 THR S 243 " model vdw 2.250 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.289 2.440 nonbonded pdb=" O LEU A 346 " pdb=" OG1 THR A 350 " model vdw 2.294 2.440 nonbonded pdb=" NE2 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.306 2.520 ... (remaining 68330 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: 0.380 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.006 0.100 9219 Z= 0.415 Angle : 0.847 10.497 12513 Z= 0.558 Chirality : 0.056 0.334 1415 Planarity : 0.005 0.049 1577 Dihedral : 16.671 87.770 3295 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.64 % Allowed : 22.87 % Favored : 75.49 % 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: -0.20 (0.25), residues: 1126 helix: 1.42 (0.28), residues: 368 sheet: 0.60 (0.33), residues: 251 loop : -1.78 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.021 0.001 PHE B 241 TYR 0.012 0.002 TYR A 47 ARG 0.005 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.004 Fit side-chains REVERT: B 251 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7456 (mtt90) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.2788 time to fit residues: 37.0672 Evaluate side-chains 96 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 425 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 ASN S 82 GLN S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9219 Z= 0.222 Angle : 0.571 8.829 12513 Z= 0.306 Chirality : 0.043 0.150 1415 Planarity : 0.004 0.046 1577 Dihedral : 5.267 53.580 1274 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.79 % Allowed : 22.46 % Favored : 73.74 % 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: 0.01 (0.25), residues: 1126 helix: 1.63 (0.27), residues: 376 sheet: 0.53 (0.31), residues: 270 loop : -1.70 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE B 241 TYR 0.019 0.002 TYR S 235 ARG 0.003 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 93 time to evaluate : 0.992 Fit side-chains REVERT: A 233 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8047 (p0) REVERT: A 297 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7132 (tp) REVERT: B 119 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8835 (m-40) REVERT: B 151 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7585 (t80) REVERT: R 470 LYS cc_start: 0.5830 (mptt) cc_final: 0.5063 (tttp) outliers start: 37 outliers final: 25 residues processed: 121 average time/residue: 0.2538 time to fit residues: 41.4052 Evaluate side-chains 118 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain Y residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 40.0000 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9219 Z= 0.155 Angle : 0.504 8.415 12513 Z= 0.269 Chirality : 0.041 0.142 1415 Planarity : 0.004 0.046 1577 Dihedral : 4.524 44.241 1266 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.90 % Allowed : 22.77 % Favored : 73.33 % 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: 1126 helix: 1.98 (0.27), residues: 376 sheet: 0.55 (0.31), residues: 276 loop : -1.67 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 234 TYR 0.015 0.001 TYR S 235 ARG 0.003 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 1.038 Fit side-chains REVERT: A 233 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7956 (p0) REVERT: A 297 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7204 (tp) REVERT: B 151 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7563 (t80) REVERT: R 470 LYS cc_start: 0.5853 (mptt) cc_final: 0.5089 (tttp) outliers start: 38 outliers final: 25 residues processed: 124 average time/residue: 0.2587 time to fit residues: 42.5313 Evaluate side-chains 116 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain Y residue 6 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.0050 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9219 Z= 0.191 Angle : 0.526 7.922 12513 Z= 0.280 Chirality : 0.042 0.140 1415 Planarity : 0.004 0.046 1577 Dihedral : 4.484 42.157 1265 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.82 % Allowed : 22.36 % Favored : 72.82 % 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: 0.26 (0.25), residues: 1126 helix: 1.99 (0.27), residues: 376 sheet: 0.53 (0.32), residues: 277 loop : -1.63 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE B 241 TYR 0.015 0.001 TYR A 47 ARG 0.004 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 95 time to evaluate : 0.915 Fit side-chains REVERT: A 233 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7970 (p0) REVERT: A 297 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7216 (tp) REVERT: B 151 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7589 (t80) REVERT: B 186 ASP cc_start: 0.7981 (p0) cc_final: 0.7637 (p0) REVERT: B 259 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: R 470 LYS cc_start: 0.5849 (mptt) cc_final: 0.5117 (tttp) REVERT: S 38 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7939 (ptm160) outliers start: 47 outliers final: 34 residues processed: 136 average time/residue: 0.2404 time to fit residues: 43.3674 Evaluate side-chains 132 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 93 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 0.0570 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9219 Z= 0.153 Angle : 0.493 7.310 12513 Z= 0.263 Chirality : 0.041 0.138 1415 Planarity : 0.003 0.043 1577 Dihedral : 4.183 37.242 1262 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.92 % Allowed : 22.15 % Favored : 72.92 % 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: 0.36 (0.25), residues: 1126 helix: 2.14 (0.28), residues: 376 sheet: 0.57 (0.32), residues: 277 loop : -1.63 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 222 TYR 0.014 0.001 TYR S 190 ARG 0.003 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 96 time to evaluate : 1.033 Fit side-chains REVERT: A 233 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7893 (p0) REVERT: A 297 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7216 (tp) REVERT: B 151 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7545 (t80) REVERT: B 186 ASP cc_start: 0.8014 (p0) cc_final: 0.7636 (p0) REVERT: B 217 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7486 (ptt) REVERT: B 259 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: R 470 LYS cc_start: 0.5839 (mptt) cc_final: 0.5129 (tttp) outliers start: 48 outliers final: 37 residues processed: 137 average time/residue: 0.2446 time to fit residues: 44.6361 Evaluate side-chains 134 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 92 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0370 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.0020 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 40.0000 chunk 104 optimal weight: 10.0000 overall best weight: 0.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 49 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9219 Z= 0.111 Angle : 0.460 10.856 12513 Z= 0.238 Chirality : 0.040 0.254 1415 Planarity : 0.003 0.038 1577 Dihedral : 3.765 25.184 1262 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.28 % Allowed : 24.10 % Favored : 72.62 % 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: 0.60 (0.25), residues: 1126 helix: 2.52 (0.28), residues: 371 sheet: 0.76 (0.32), residues: 272 loop : -1.63 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE A 222 TYR 0.020 0.001 TYR S 60 ARG 0.003 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 0.955 Fit side-chains REVERT: B 151 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7618 (t80) REVERT: B 259 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: R 470 LYS cc_start: 0.5820 (mptt) cc_final: 0.5153 (tttp) REVERT: S 116 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7590 (m) REVERT: S 119 VAL cc_start: 0.8179 (t) cc_final: 0.7928 (m) outliers start: 32 outliers final: 17 residues processed: 137 average time/residue: 0.2397 time to fit residues: 44.0698 Evaluate side-chains 123 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0770 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 66 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9219 Z= 0.120 Angle : 0.476 12.894 12513 Z= 0.244 Chirality : 0.040 0.154 1415 Planarity : 0.003 0.036 1577 Dihedral : 3.592 22.801 1259 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.46 % Allowed : 24.92 % Favored : 72.62 % 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: 0.66 (0.26), residues: 1126 helix: 2.54 (0.28), residues: 374 sheet: 0.79 (0.32), residues: 272 loop : -1.58 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.013 0.001 TYR S 190 ARG 0.005 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.033 Fit side-chains REVERT: B 151 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7634 (t80) REVERT: R 470 LYS cc_start: 0.6027 (mptt) cc_final: 0.5272 (tttp) REVERT: S 116 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7599 (m) REVERT: S 119 VAL cc_start: 0.8148 (t) cc_final: 0.7892 (m) outliers start: 24 outliers final: 17 residues processed: 125 average time/residue: 0.2390 time to fit residues: 40.2100 Evaluate side-chains 121 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9219 Z= 0.144 Angle : 0.494 11.400 12513 Z= 0.255 Chirality : 0.041 0.171 1415 Planarity : 0.003 0.037 1577 Dihedral : 3.714 23.119 1259 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.18 % Allowed : 24.21 % Favored : 72.62 % 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: 0.65 (0.26), residues: 1126 helix: 2.52 (0.28), residues: 374 sheet: 0.70 (0.32), residues: 277 loop : -1.54 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR A 47 ARG 0.004 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.965 Fit side-chains REVERT: B 151 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7665 (t80) REVERT: B 186 ASP cc_start: 0.8035 (p0) cc_final: 0.7551 (p0) REVERT: R 470 LYS cc_start: 0.6049 (mptt) cc_final: 0.5262 (tttp) REVERT: S 116 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7599 (m) REVERT: S 119 VAL cc_start: 0.8197 (t) cc_final: 0.7934 (m) outliers start: 31 outliers final: 21 residues processed: 126 average time/residue: 0.2497 time to fit residues: 41.8082 Evaluate side-chains 121 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9219 Z= 0.118 Angle : 0.483 15.531 12513 Z= 0.245 Chirality : 0.040 0.137 1415 Planarity : 0.003 0.035 1577 Dihedral : 3.616 23.120 1259 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.67 % Allowed : 24.72 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1126 helix: 2.62 (0.28), residues: 374 sheet: 0.74 (0.32), residues: 277 loop : -1.53 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 222 TYR 0.012 0.001 TYR S 60 ARG 0.004 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.985 Fit side-chains REVERT: B 151 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7650 (t80) REVERT: B 186 ASP cc_start: 0.8033 (p0) cc_final: 0.7642 (p0) REVERT: B 259 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: R 470 LYS cc_start: 0.6092 (mptt) cc_final: 0.5264 (tttp) REVERT: S 116 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7619 (m) REVERT: S 119 VAL cc_start: 0.8149 (t) cc_final: 0.7892 (m) outliers start: 26 outliers final: 21 residues processed: 125 average time/residue: 0.2468 time to fit residues: 41.2640 Evaluate side-chains 122 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 0.1980 chunk 102 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9219 Z= 0.169 Angle : 0.517 14.542 12513 Z= 0.265 Chirality : 0.041 0.143 1415 Planarity : 0.003 0.037 1577 Dihedral : 3.772 23.355 1259 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.56 % Allowed : 24.92 % Favored : 72.51 % 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: 0.62 (0.26), residues: 1126 helix: 2.49 (0.28), residues: 374 sheet: 0.68 (0.32), residues: 278 loop : -1.55 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE B 241 TYR 0.016 0.001 TYR A 47 ARG 0.004 0.000 ARG Y 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.030 Fit side-chains REVERT: B 151 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7597 (t80) REVERT: B 186 ASP cc_start: 0.8095 (p0) cc_final: 0.7591 (p0) REVERT: B 217 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7449 (ptt) REVERT: R 470 LYS cc_start: 0.6110 (mptt) cc_final: 0.5265 (tttp) outliers start: 25 outliers final: 21 residues processed: 123 average time/residue: 0.2774 time to fit residues: 45.4629 Evaluate side-chains 125 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.163079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127005 restraints weight = 10149.010| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.79 r_work: 0.3087 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9219 Z= 0.132 Angle : 0.490 14.279 12513 Z= 0.251 Chirality : 0.040 0.141 1415 Planarity : 0.003 0.035 1577 Dihedral : 3.698 23.353 1259 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.87 % Allowed : 24.51 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1126 helix: 2.59 (0.28), residues: 374 sheet: 0.70 (0.32), residues: 278 loop : -1.54 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR A 47 ARG 0.005 0.000 ARG R 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.04 seconds wall clock time: 37 minutes 11.35 seconds (2231.35 seconds total)