Starting phenix.real_space_refine on Sat Apr 6 19:04:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/04_2024/8j6i_36005_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/04_2024/8j6i_36005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/04_2024/8j6i_36005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/04_2024/8j6i_36005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/04_2024/8j6i_36005_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/04_2024/8j6i_36005_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5630 2.51 5 N 1501 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 267": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8801 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1748 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 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: "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: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 405 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} 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': 2, 'ARG:plan': 1, 'GLU%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1737 Classifications: {'peptide': 233} Modifications used: {'COO': 1} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.58 Number of scatterers: 8801 At special positions: 0 Unit cell: (107.12, 110.416, 129.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1605 8.00 N 1501 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.03 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: 3.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 32.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'R' and resid 26 through 54 Proline residue: R 31 - end of helix removed outlier: 3.843A pdb=" N GLY R 44 " --> pdb=" O PHE R 40 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 78 removed outlier: 4.194A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 88 Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 141 through 164 removed outlier: 3.577A pdb=" N THR R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 163 " --> pdb=" O THR R 159 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 216 removed outlier: 3.542A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 227 through 244 removed outlier: 3.772A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 260 removed outlier: 3.639A pdb=" N ARG R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 294 removed outlier: 4.017A pdb=" N LEU R 280 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.069A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.911A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.537A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 13 through 24 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.632A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.186A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.105A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.989A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.900A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.575A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 52 removed outlier: 7.128A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.198A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.542A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.889A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 93 through 99 removed outlier: 3.558A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.656A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.038A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 226 " --> pdb=" O GLN H 179 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR H 175 " --> pdb=" O MET H 230 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1011 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: 2.40 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1407 1.31 - 1.44: 2526 1.44 - 1.57: 4967 1.57 - 1.70: 4 1.70 - 1.82: 92 Bond restraints: 8996 Sorted by residual: bond pdb=" C20 FI7 R 401 " pdb=" C21 FI7 R 401 " ideal model delta sigma weight residual 1.355 1.590 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C26 FI7 R 401 " pdb=" C27 FI7 R 401 " ideal model delta sigma weight residual 1.516 1.344 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C13 FI7 R 401 " pdb=" N14 FI7 R 401 " ideal model delta sigma weight residual 1.320 1.474 -0.154 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C08 FI7 R 401 " pdb=" C09 FI7 R 401 " ideal model delta sigma weight residual 1.393 1.542 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C08 FI7 R 401 " pdb=" N14 FI7 R 401 " ideal model delta sigma weight residual 1.327 1.469 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 8991 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.83: 188 106.83 - 113.65: 4942 113.65 - 120.47: 3455 120.47 - 127.30: 3515 127.30 - 134.12: 96 Bond angle restraints: 12196 Sorted by residual: angle pdb=" N TYR R 269 " pdb=" CA TYR R 269 " pdb=" C TYR R 269 " ideal model delta sigma weight residual 111.11 104.72 6.39 1.20e+00 6.94e-01 2.83e+01 angle pdb=" C LEU R 80 " pdb=" N PRO R 81 " pdb=" CD PRO R 81 " ideal model delta sigma weight residual 125.00 105.29 19.71 4.10e+00 5.95e-02 2.31e+01 angle pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " pdb=" C20 FI7 R 401 " ideal model delta sigma weight residual 130.45 116.24 14.21 3.00e+00 1.11e-01 2.25e+01 angle pdb=" CA PRO R 81 " pdb=" N PRO R 81 " pdb=" CD PRO R 81 " ideal model delta sigma weight residual 112.00 117.45 -5.45 1.40e+00 5.10e-01 1.51e+01 angle pdb=" C ILE R 13 " pdb=" N ASP R 14 " pdb=" CA ASP R 14 " ideal model delta sigma weight residual 123.91 117.63 6.28 1.66e+00 3.63e-01 1.43e+01 ... (remaining 12191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.24: 4882 25.24 - 50.49: 390 50.49 - 75.73: 34 75.73 - 100.97: 4 100.97 - 126.21: 2 Dihedral angle restraints: 5312 sinusoidal: 2037 harmonic: 3275 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 132.79 -39.79 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" C25 FI7 R 401 " pdb=" C26 FI7 R 401 " pdb=" C27 FI7 R 401 " pdb=" C28 FI7 R 401 " ideal model delta sinusoidal sigma weight residual 63.14 -63.07 126.21 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C20 FI7 R 401 " pdb=" C27 FI7 R 401 " pdb=" C28 FI7 R 401 " pdb=" C26 FI7 R 401 " ideal model delta sinusoidal sigma weight residual 45.86 -56.98 102.84 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 5309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1205 0.054 - 0.108: 136 0.108 - 0.163: 38 0.163 - 0.217: 0 0.217 - 0.271: 2 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA TYR R 269 " pdb=" N TYR R 269 " pdb=" C TYR R 269 " pdb=" CB TYR R 269 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE R 13 " pdb=" N ILE R 13 " pdb=" C ILE R 13 " pdb=" CB ILE R 13 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA TYR H 235 " pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CB TYR H 235 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1378 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " 0.086 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO R 81 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 239 " -0.008 2.00e-02 2.50e+03 1.14e-02 2.28e+00 pdb=" CG PHE H 239 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE H 239 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 239 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE H 239 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 239 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 239 " -0.004 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 347 2.71 - 3.26: 8889 3.26 - 3.81: 14184 3.81 - 4.35: 17397 4.35 - 4.90: 29689 Nonbonded interactions: 70506 Sorted by model distance: nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.167 2.440 nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.248 2.440 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.262 2.520 nonbonded pdb=" O ASP B 247 " pdb=" OD1 ASP B 247 " model vdw 2.264 3.040 ... (remaining 70501 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: 0.750 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: 3.930 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.450 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 0.235 8996 Z= 0.421 Angle : 0.626 19.710 12196 Z= 0.313 Chirality : 0.040 0.271 1381 Planarity : 0.005 0.146 1538 Dihedral : 16.601 126.213 3185 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 25.99 % Favored : 74.01 % 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: 1.37 (0.27), residues: 1113 helix: 2.35 (0.28), residues: 365 sheet: 1.30 (0.34), residues: 252 loop : -0.41 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 93 HIS 0.004 0.000 HIS R 189 PHE 0.023 0.001 PHE H 239 TYR 0.015 0.001 TYR H 235 ARG 0.005 0.000 ARG R 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.964 Fit side-chains REVERT: R 23 ASP cc_start: 0.5249 (t70) cc_final: 0.4522 (t0) REVERT: R 86 ASN cc_start: 0.5355 (t0) cc_final: 0.4945 (m110) REVERT: R 112 GLN cc_start: 0.6961 (tp40) cc_final: 0.6564 (mm-40) REVERT: R 141 ASN cc_start: 0.5635 (m110) cc_final: 0.5373 (m-40) REVERT: R 227 LYS cc_start: 0.5514 (mtmm) cc_final: 0.5206 (mtpt) REVERT: R 285 MET cc_start: 0.6969 (ttp) cc_final: 0.6581 (ttp) REVERT: R 290 ASP cc_start: 0.7039 (m-30) cc_final: 0.6710 (t70) REVERT: A 195 HIS cc_start: 0.7710 (t70) cc_final: 0.7358 (t-170) REVERT: A 197 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7432 (mttt) REVERT: A 198 MET cc_start: 0.8481 (ttm) cc_final: 0.8246 (ttp) REVERT: A 276 GLU cc_start: 0.6616 (mm-30) cc_final: 0.5968 (mt-10) REVERT: A 305 CYS cc_start: 0.7644 (m) cc_final: 0.6602 (t) REVERT: A 321 THR cc_start: 0.8904 (t) cc_final: 0.8517 (m) REVERT: A 330 LYS cc_start: 0.7417 (mttt) cc_final: 0.7047 (tptt) REVERT: A 349 LYS cc_start: 0.7152 (ttmm) cc_final: 0.6352 (tppt) REVERT: B 46 ARG cc_start: 0.7402 (mtp85) cc_final: 0.7057 (mtp-110) REVERT: B 217 MET cc_start: 0.6776 (pmm) cc_final: 0.5839 (pp-130) REVERT: B 220 GLN cc_start: 0.8300 (mp10) cc_final: 0.8063 (mt0) REVERT: B 230 ASN cc_start: 0.7390 (t0) cc_final: 0.7149 (m-40) REVERT: B 295 ASN cc_start: 0.7403 (m-40) cc_final: 0.7037 (m110) REVERT: B 325 MET cc_start: 0.8172 (tpp) cc_final: 0.7875 (mmm) REVERT: H 69 THR cc_start: 0.6352 (t) cc_final: 0.5795 (m) REVERT: H 82 GLN cc_start: 0.7600 (tp40) cc_final: 0.7339 (tp40) REVERT: H 195 LEU cc_start: 0.7729 (mp) cc_final: 0.7501 (mt) REVERT: H 230 MET cc_start: 0.7464 (tpp) cc_final: 0.6981 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 1.0955 time to fit residues: 219.7169 Evaluate side-chains 117 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 176 GLN G 18 GLN H 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8996 Z= 0.314 Angle : 0.662 9.685 12196 Z= 0.343 Chirality : 0.045 0.207 1381 Planarity : 0.005 0.042 1538 Dihedral : 5.984 63.381 1244 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 6.20 % Allowed : 22.99 % Favored : 70.80 % 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: 0.99 (0.26), residues: 1113 helix: 1.87 (0.27), residues: 365 sheet: 0.90 (0.32), residues: 286 loop : -0.46 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.019 0.002 PHE A 196 TYR 0.026 0.002 TYR H 235 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 133 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: R 23 ASP cc_start: 0.5517 (t70) cc_final: 0.4975 (t0) REVERT: R 25 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6222 (t80) REVERT: R 86 ASN cc_start: 0.5714 (t0) cc_final: 0.5359 (m110) REVERT: R 94 LYS cc_start: 0.4685 (OUTLIER) cc_final: 0.4377 (mtmm) REVERT: R 227 LYS cc_start: 0.5768 (mtmm) cc_final: 0.5376 (pttt) REVERT: R 238 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.5922 (mt) REVERT: A 18 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7037 (mmm) REVERT: A 197 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8004 (mttt) REVERT: A 198 MET cc_start: 0.8790 (ttm) cc_final: 0.8529 (ttm) REVERT: A 207 GLU cc_start: 0.7106 (tt0) cc_final: 0.6488 (mt-10) REVERT: A 276 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6506 (mt-10) REVERT: A 312 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7675 (mptm) REVERT: A 321 THR cc_start: 0.8886 (t) cc_final: 0.8537 (m) REVERT: A 349 LYS cc_start: 0.7522 (ttmm) cc_final: 0.6685 (tppt) REVERT: B 120 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7381 (mm) REVERT: B 134 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7290 (ptt-90) REVERT: B 234 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: B 325 MET cc_start: 0.8301 (tpp) cc_final: 0.8040 (mmm) REVERT: B 333 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: H 30 SER cc_start: 0.7786 (t) cc_final: 0.7432 (p) REVERT: H 82 GLN cc_start: 0.7879 (tp40) cc_final: 0.7668 (tp40) REVERT: H 195 LEU cc_start: 0.7941 (mp) cc_final: 0.7656 (mt) REVERT: H 230 MET cc_start: 0.7757 (tpp) cc_final: 0.7312 (mmm) outliers start: 58 outliers final: 18 residues processed: 168 average time/residue: 1.0281 time to fit residues: 186.0693 Evaluate side-chains 130 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 0.0170 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN G 24 ASN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8996 Z= 0.160 Angle : 0.528 6.225 12196 Z= 0.274 Chirality : 0.041 0.163 1381 Planarity : 0.004 0.044 1538 Dihedral : 4.834 59.243 1244 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 4.92 % Allowed : 25.03 % Favored : 70.05 % 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: 0.94 (0.26), residues: 1113 helix: 1.87 (0.28), residues: 368 sheet: 0.90 (0.32), residues: 278 loop : -0.54 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 195 PHE 0.024 0.001 PHE R 186 TYR 0.023 0.001 TYR H 235 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: R 25 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.6278 (t80) REVERT: R 86 ASN cc_start: 0.5557 (t0) cc_final: 0.5130 (m-40) REVERT: R 227 LYS cc_start: 0.5753 (mtmm) cc_final: 0.5443 (pttt) REVERT: A 18 MET cc_start: 0.7157 (ttp) cc_final: 0.6952 (mmm) REVERT: A 25 GLU cc_start: 0.7522 (tt0) cc_final: 0.7291 (mt-10) REVERT: A 33 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6802 (mm-30) REVERT: A 52 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6822 (tp40) REVERT: A 197 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8007 (mttt) REVERT: A 198 MET cc_start: 0.8849 (ttm) cc_final: 0.8590 (ttp) REVERT: A 207 GLU cc_start: 0.7068 (tt0) cc_final: 0.6529 (mt-10) REVERT: A 276 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6505 (mt-10) REVERT: A 305 CYS cc_start: 0.7491 (m) cc_final: 0.6615 (t) REVERT: A 321 THR cc_start: 0.8808 (t) cc_final: 0.8492 (m) REVERT: A 349 LYS cc_start: 0.7583 (ttmm) cc_final: 0.6732 (tppt) REVERT: B 120 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7065 (mm) REVERT: B 134 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7130 (ptt-90) REVERT: B 325 MET cc_start: 0.8282 (tpp) cc_final: 0.7999 (mmm) REVERT: H 30 SER cc_start: 0.7849 (t) cc_final: 0.7495 (p) REVERT: H 195 LEU cc_start: 0.7911 (mp) cc_final: 0.7571 (mt) REVERT: H 230 MET cc_start: 0.7647 (tpp) cc_final: 0.7222 (mmm) outliers start: 46 outliers final: 13 residues processed: 138 average time/residue: 1.1051 time to fit residues: 163.9936 Evaluate side-chains 114 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 GLN A 322 HIS B 230 ASN B 237 ASN H 82 GLN H 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8996 Z= 0.242 Angle : 0.571 8.289 12196 Z= 0.297 Chirality : 0.042 0.187 1381 Planarity : 0.004 0.046 1538 Dihedral : 5.000 52.401 1244 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 6.20 % Allowed : 23.85 % Favored : 69.95 % 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: 0.79 (0.26), residues: 1113 helix: 1.73 (0.28), residues: 369 sheet: 0.78 (0.31), residues: 281 loop : -0.60 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS H 35 PHE 0.025 0.002 PHE R 186 TYR 0.025 0.001 TYR H 235 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 108 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: R 112 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: R 162 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5402 (pp) REVERT: R 227 LYS cc_start: 0.6043 (mtmm) cc_final: 0.5694 (pttt) REVERT: A 25 GLU cc_start: 0.7542 (tt0) cc_final: 0.7284 (mt-10) REVERT: A 33 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: A 52 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6888 (tp40) REVERT: A 197 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8267 (mtpt) REVERT: A 198 MET cc_start: 0.8836 (ttm) cc_final: 0.8613 (ttm) REVERT: A 207 GLU cc_start: 0.7223 (tt0) cc_final: 0.6522 (mt-10) REVERT: A 276 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6571 (mt-10) REVERT: A 305 CYS cc_start: 0.7612 (m) cc_final: 0.6736 (t) REVERT: A 312 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7628 (mptm) REVERT: A 321 THR cc_start: 0.8812 (t) cc_final: 0.8589 (m) REVERT: A 349 LYS cc_start: 0.7737 (ttmm) cc_final: 0.6881 (tppt) REVERT: B 120 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7144 (mm) REVERT: B 134 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7475 (ptt-90) REVERT: B 234 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: B 258 ASP cc_start: 0.7201 (p0) cc_final: 0.6889 (p0) REVERT: H 30 SER cc_start: 0.8071 (t) cc_final: 0.7714 (p) REVERT: H 195 LEU cc_start: 0.7905 (mp) cc_final: 0.7546 (mt) REVERT: H 230 MET cc_start: 0.7635 (tpp) cc_final: 0.7351 (mmm) REVERT: H 233 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7104 (mt) outliers start: 58 outliers final: 25 residues processed: 149 average time/residue: 1.0444 time to fit residues: 167.8700 Evaluate side-chains 134 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN B 237 ASN B 259 GLN H 82 GLN H 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8996 Z= 0.293 Angle : 0.597 9.262 12196 Z= 0.312 Chirality : 0.044 0.199 1381 Planarity : 0.004 0.047 1538 Dihedral : 5.159 54.009 1244 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 5.99 % Allowed : 23.74 % Favored : 70.27 % 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: 0.63 (0.26), residues: 1113 helix: 1.58 (0.28), residues: 370 sheet: 0.61 (0.31), residues: 287 loop : -0.64 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.023 0.002 PHE R 186 TYR 0.028 0.002 TYR H 235 ARG 0.003 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 109 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: R 94 LYS cc_start: 0.4942 (OUTLIER) cc_final: 0.4622 (mtmm) REVERT: A 24 ARG cc_start: 0.7109 (tpp-160) cc_final: 0.6578 (ttm110) REVERT: A 25 GLU cc_start: 0.7556 (tt0) cc_final: 0.7296 (mt-10) REVERT: A 33 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: A 52 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.7013 (tp40) REVERT: A 197 LYS cc_start: 0.8705 (mtmt) cc_final: 0.7739 (mttt) REVERT: A 207 GLU cc_start: 0.7288 (tt0) cc_final: 0.6522 (mt-10) REVERT: A 276 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6729 (mt-10) REVERT: A 305 CYS cc_start: 0.7547 (m) cc_final: 0.6799 (t) REVERT: A 312 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7531 (mptm) REVERT: A 321 THR cc_start: 0.8885 (t) cc_final: 0.8651 (m) REVERT: A 349 LYS cc_start: 0.7743 (ttmm) cc_final: 0.6959 (tppt) REVERT: B 23 LYS cc_start: 0.8018 (tptt) cc_final: 0.7618 (ttpt) REVERT: B 134 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7495 (ptt-90) REVERT: G 37 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (mp) REVERT: H 30 SER cc_start: 0.8178 (t) cc_final: 0.7843 (p) REVERT: H 195 LEU cc_start: 0.7908 (mp) cc_final: 0.7528 (mt) REVERT: H 230 MET cc_start: 0.7727 (tpp) cc_final: 0.7481 (mmm) REVERT: H 233 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7109 (mt) outliers start: 56 outliers final: 32 residues processed: 152 average time/residue: 1.1617 time to fit residues: 190.3226 Evaluate side-chains 142 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 103 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 GLN B 175 GLN B 237 ASN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8996 Z= 0.175 Angle : 0.522 6.467 12196 Z= 0.275 Chirality : 0.041 0.175 1381 Planarity : 0.004 0.050 1538 Dihedral : 4.833 53.169 1244 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 5.35 % Allowed : 24.71 % Favored : 69.95 % 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: 0.74 (0.26), residues: 1113 helix: 1.71 (0.28), residues: 366 sheet: 0.75 (0.31), residues: 277 loop : -0.63 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 195 PHE 0.025 0.001 PHE R 186 TYR 0.023 0.001 TYR H 235 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 113 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: R 84 MET cc_start: 0.4482 (tpt) cc_final: 0.4109 (tpt) REVERT: R 94 LYS cc_start: 0.4851 (OUTLIER) cc_final: 0.4569 (mtmm) REVERT: A 24 ARG cc_start: 0.7078 (tpp-160) cc_final: 0.6557 (ttm110) REVERT: A 25 GLU cc_start: 0.7553 (tt0) cc_final: 0.7284 (mt-10) REVERT: A 33 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: A 197 LYS cc_start: 0.8702 (mtmt) cc_final: 0.7726 (mttt) REVERT: A 207 GLU cc_start: 0.7232 (tt0) cc_final: 0.6468 (mt-10) REVERT: A 276 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6728 (mt-10) REVERT: A 305 CYS cc_start: 0.7538 (m) cc_final: 0.6828 (t) REVERT: A 312 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7464 (mptm) REVERT: A 321 THR cc_start: 0.8796 (t) cc_final: 0.8582 (m) REVERT: A 349 LYS cc_start: 0.7786 (ttmm) cc_final: 0.6990 (tppt) REVERT: B 23 LYS cc_start: 0.8040 (tptt) cc_final: 0.7619 (ttpt) REVERT: B 134 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7404 (ptt-90) REVERT: B 234 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: B 325 MET cc_start: 0.8167 (tpp) cc_final: 0.7909 (mmt) REVERT: H 30 SER cc_start: 0.8164 (t) cc_final: 0.7838 (p) REVERT: H 34 MET cc_start: 0.8117 (mmp) cc_final: 0.7874 (mmm) REVERT: H 195 LEU cc_start: 0.7956 (mp) cc_final: 0.7602 (mt) REVERT: H 230 MET cc_start: 0.7740 (tpp) cc_final: 0.7398 (mmm) outliers start: 50 outliers final: 28 residues processed: 147 average time/residue: 1.1463 time to fit residues: 180.6432 Evaluate side-chains 139 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 GLN B 237 ASN H 82 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8996 Z= 0.151 Angle : 0.496 5.838 12196 Z= 0.262 Chirality : 0.040 0.169 1381 Planarity : 0.004 0.051 1538 Dihedral : 4.611 51.837 1244 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 5.24 % Allowed : 25.24 % Favored : 69.52 % 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: 0.79 (0.26), residues: 1113 helix: 1.70 (0.28), residues: 371 sheet: 0.75 (0.32), residues: 281 loop : -0.57 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS A 195 PHE 0.025 0.001 PHE R 186 TYR 0.021 0.001 TYR H 235 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: R 73 ASP cc_start: 0.5312 (OUTLIER) cc_final: 0.4885 (m-30) REVERT: R 84 MET cc_start: 0.4387 (tpt) cc_final: 0.4036 (tpt) REVERT: R 94 LYS cc_start: 0.4580 (OUTLIER) cc_final: 0.4256 (mtmm) REVERT: R 162 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5266 (pp) REVERT: A 24 ARG cc_start: 0.7050 (tpp-160) cc_final: 0.6511 (ttm110) REVERT: A 25 GLU cc_start: 0.7563 (tt0) cc_final: 0.7294 (mt-10) REVERT: A 33 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: A 197 LYS cc_start: 0.8673 (mtmt) cc_final: 0.7685 (mttt) REVERT: A 207 GLU cc_start: 0.7200 (tt0) cc_final: 0.6412 (mt-10) REVERT: A 276 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6747 (mt-10) REVERT: A 305 CYS cc_start: 0.7602 (m) cc_final: 0.7054 (t) REVERT: A 349 LYS cc_start: 0.7756 (ttmm) cc_final: 0.6954 (tppt) REVERT: B 23 LYS cc_start: 0.7986 (tptt) cc_final: 0.7584 (ttpt) REVERT: B 50 THR cc_start: 0.8799 (t) cc_final: 0.8475 (m) REVERT: B 134 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7332 (ptt-90) REVERT: B 234 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: H 30 SER cc_start: 0.8208 (t) cc_final: 0.7880 (p) REVERT: H 34 MET cc_start: 0.8072 (mmp) cc_final: 0.7823 (mmm) REVERT: H 195 LEU cc_start: 0.7899 (mp) cc_final: 0.7559 (mt) REVERT: H 230 MET cc_start: 0.7669 (tpp) cc_final: 0.7377 (mmm) outliers start: 49 outliers final: 28 residues processed: 148 average time/residue: 1.1145 time to fit residues: 177.6249 Evaluate side-chains 145 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 237 ASN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8996 Z= 0.250 Angle : 0.560 8.472 12196 Z= 0.294 Chirality : 0.042 0.184 1381 Planarity : 0.004 0.050 1538 Dihedral : 4.949 52.061 1244 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 5.13 % Allowed : 25.56 % Favored : 69.30 % 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: 1113 helix: 1.61 (0.28), residues: 373 sheet: 0.56 (0.31), residues: 286 loop : -0.59 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.024 0.002 PHE R 186 TYR 0.025 0.001 TYR H 235 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: R 23 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.6212 (m-30) REVERT: R 73 ASP cc_start: 0.5325 (OUTLIER) cc_final: 0.4852 (m-30) REVERT: R 84 MET cc_start: 0.4407 (tpt) cc_final: 0.4097 (tpt) REVERT: R 94 LYS cc_start: 0.4828 (OUTLIER) cc_final: 0.4496 (mtmm) REVERT: R 103 MET cc_start: 0.5887 (ttp) cc_final: 0.5280 (ttt) REVERT: R 162 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5367 (pp) REVERT: A 24 ARG cc_start: 0.7118 (tpp-160) cc_final: 0.6597 (ttm110) REVERT: A 25 GLU cc_start: 0.7554 (tt0) cc_final: 0.7288 (mt-10) REVERT: A 33 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: A 197 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8350 (mtpt) REVERT: A 207 GLU cc_start: 0.7404 (tt0) cc_final: 0.6550 (mt-10) REVERT: A 276 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6786 (mt-10) REVERT: A 305 CYS cc_start: 0.7655 (m) cc_final: 0.6975 (t) REVERT: A 349 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7084 (tppt) REVERT: B 23 LYS cc_start: 0.8001 (tptt) cc_final: 0.7614 (ttpt) REVERT: B 61 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7966 (ppp) REVERT: B 129 ARG cc_start: 0.7377 (ptt90) cc_final: 0.7136 (ttt90) REVERT: B 134 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7433 (ptt-90) REVERT: H 30 SER cc_start: 0.8271 (t) cc_final: 0.7967 (p) REVERT: H 34 MET cc_start: 0.8175 (mmp) cc_final: 0.7904 (mmm) REVERT: H 139 VAL cc_start: 0.8357 (m) cc_final: 0.8113 (p) REVERT: H 192 MET cc_start: 0.7283 (ptm) cc_final: 0.7045 (pp-130) REVERT: H 195 LEU cc_start: 0.7963 (mp) cc_final: 0.7621 (mt) REVERT: H 230 MET cc_start: 0.7748 (tpp) cc_final: 0.7493 (mmm) outliers start: 48 outliers final: 24 residues processed: 142 average time/residue: 1.1306 time to fit residues: 172.5218 Evaluate side-chains 142 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 GLN A 294 ASN B 237 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8996 Z= 0.174 Angle : 0.514 6.338 12196 Z= 0.270 Chirality : 0.041 0.163 1381 Planarity : 0.004 0.051 1538 Dihedral : 4.751 52.116 1244 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 4.60 % Allowed : 26.42 % Favored : 68.98 % 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: 0.68 (0.26), residues: 1113 helix: 1.69 (0.28), residues: 369 sheet: 0.56 (0.31), residues: 279 loop : -0.60 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 195 PHE 0.024 0.001 PHE R 186 TYR 0.023 0.001 TYR H 235 ARG 0.008 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 113 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: R 73 ASP cc_start: 0.5286 (OUTLIER) cc_final: 0.4807 (m-30) REVERT: R 84 MET cc_start: 0.4419 (tpt) cc_final: 0.4078 (tpt) REVERT: R 94 LYS cc_start: 0.4755 (OUTLIER) cc_final: 0.4269 (mtmm) REVERT: R 162 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5293 (pp) REVERT: R 189 HIS cc_start: 0.6088 (OUTLIER) cc_final: 0.5772 (p90) REVERT: R 214 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8335 (t) REVERT: A 24 ARG cc_start: 0.7095 (tpp-160) cc_final: 0.6581 (ttm110) REVERT: A 25 GLU cc_start: 0.7556 (tt0) cc_final: 0.7298 (mt-10) REVERT: A 33 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: A 197 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8325 (mtmt) REVERT: A 207 GLU cc_start: 0.7405 (tt0) cc_final: 0.6548 (mt-10) REVERT: A 276 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6929 (mt-10) REVERT: A 305 CYS cc_start: 0.7652 (m) cc_final: 0.7018 (t) REVERT: A 349 LYS cc_start: 0.7838 (ttmm) cc_final: 0.6991 (tppt) REVERT: B 23 LYS cc_start: 0.7923 (tptt) cc_final: 0.7500 (ttpm) REVERT: B 61 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7919 (ppp) REVERT: B 134 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7343 (ptt-90) REVERT: H 30 SER cc_start: 0.8258 (t) cc_final: 0.7948 (p) REVERT: H 34 MET cc_start: 0.8102 (mmp) cc_final: 0.7868 (mmm) REVERT: H 139 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8142 (p) REVERT: H 195 LEU cc_start: 0.7957 (mp) cc_final: 0.7624 (mt) outliers start: 43 outliers final: 26 residues processed: 143 average time/residue: 1.1049 time to fit residues: 169.7865 Evaluate side-chains 144 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 GLN A 294 ASN B 237 ASN G 18 GLN H 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8996 Z= 0.195 Angle : 0.527 7.299 12196 Z= 0.277 Chirality : 0.041 0.166 1381 Planarity : 0.004 0.051 1538 Dihedral : 4.771 52.186 1244 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 5.35 % Allowed : 25.24 % Favored : 69.41 % 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: 0.65 (0.26), residues: 1113 helix: 1.64 (0.28), residues: 369 sheet: 0.57 (0.31), residues: 279 loop : -0.61 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.025 0.001 PHE R 186 TYR 0.023 0.001 TYR H 235 ARG 0.007 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 108 time to evaluate : 0.886 Fit side-chains REVERT: R 73 ASP cc_start: 0.5398 (OUTLIER) cc_final: 0.4816 (m-30) REVERT: R 84 MET cc_start: 0.4269 (tpt) cc_final: 0.3973 (tpt) REVERT: R 94 LYS cc_start: 0.4642 (OUTLIER) cc_final: 0.4280 (mtmm) REVERT: R 103 MET cc_start: 0.5866 (ttp) cc_final: 0.5337 (ttt) REVERT: R 162 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5318 (pp) REVERT: R 189 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.5764 (p90) REVERT: A 24 ARG cc_start: 0.7105 (tpp-160) cc_final: 0.6589 (ttm110) REVERT: A 25 GLU cc_start: 0.7559 (tt0) cc_final: 0.7299 (mt-10) REVERT: A 33 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: A 197 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8353 (mtpt) REVERT: A 207 GLU cc_start: 0.7452 (tt0) cc_final: 0.6573 (mt-10) REVERT: A 276 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6908 (mt-10) REVERT: A 305 CYS cc_start: 0.7650 (m) cc_final: 0.7006 (t) REVERT: A 349 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7038 (tppt) REVERT: B 23 LYS cc_start: 0.7966 (tptt) cc_final: 0.7485 (ttpm) REVERT: B 61 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7919 (ppp) REVERT: B 134 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7358 (ptt-90) REVERT: B 325 MET cc_start: 0.8167 (tpp) cc_final: 0.7948 (mmt) REVERT: G 21 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.4384 (mmp) REVERT: G 37 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8390 (mp) REVERT: H 30 SER cc_start: 0.8272 (t) cc_final: 0.7964 (p) REVERT: H 34 MET cc_start: 0.8118 (mmp) cc_final: 0.7883 (mmm) REVERT: H 139 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (p) REVERT: H 195 LEU cc_start: 0.7954 (mp) cc_final: 0.7616 (mt) outliers start: 50 outliers final: 27 residues processed: 143 average time/residue: 1.0749 time to fit residues: 165.0207 Evaluate side-chains 143 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN G 24 ASN H 113 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125835 restraints weight = 9992.774| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.93 r_work: 0.3272 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8996 Z= 0.261 Angle : 0.567 8.229 12196 Z= 0.297 Chirality : 0.043 0.183 1381 Planarity : 0.004 0.050 1538 Dihedral : 4.983 51.851 1244 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 5.24 % Allowed : 25.67 % Favored : 69.09 % 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: 1113 helix: 1.63 (0.28), residues: 366 sheet: 0.54 (0.31), residues: 287 loop : -0.51 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.024 0.002 PHE R 186 TYR 0.026 0.002 TYR H 235 ARG 0.006 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.73 seconds wall clock time: 68 minutes 33.56 seconds (4113.56 seconds total)