Starting phenix.real_space_refine on Fri Nov 15 19:40:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3z_36869/11_2024/8k3z_36869_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3z_36869/11_2024/8k3z_36869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3z_36869/11_2024/8k3z_36869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3z_36869/11_2024/8k3z_36869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3z_36869/11_2024/8k3z_36869_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3z_36869/11_2024/8k3z_36869_neut.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.131 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 6093 2.51 5 N 1622 2.21 5 O 1756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9536 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2390 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2589 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1850 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 230} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 510 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.98, per 1000 atoms: 0.63 Number of scatterers: 9536 At special positions: 0 Unit cell: (158.1, 124.1, 96.9, 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 1756 8.00 N 1622 7.00 C 6093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 186 " distance=2.04 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 50 " 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 - 3.00 Amino acid : True - 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 31 through 65 removed outlier: 3.650A pdb=" N ILE A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 72 through 90 removed outlier: 5.191A pdb=" N LEU A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.623A pdb=" N TRP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 140 removed outlier: 4.006A pdb=" N LEU A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 113 " --> pdb=" O CYS A 109 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.973A pdb=" N VAL A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 192 through 208 removed outlier: 3.764A pdb=" N VAL A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 removed outlier: 3.708A pdb=" N VAL A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 267 removed outlier: 3.838A pdb=" N ALA A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 273 through 292 removed outlier: 3.561A pdb=" N GLU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'B' and resid 9 through 24 removed outlier: 3.578A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.475A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.608A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 4.187A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.816A pdb=" N GLN C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 55 through 62 removed outlier: 3.804A pdb=" N GLN D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.619A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.596A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.688A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.046A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.166A 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: 4.131A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.989A 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 153 removed outlier: 6.719A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.923A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.727A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.720A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.242A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 28 through 29 removed outlier: 4.318A pdb=" N GLN D 37 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.011A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.223A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.534A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1197 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: 2.76 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1543 1.29 - 1.43: 2578 1.43 - 1.56: 5530 1.56 - 1.69: 0 1.69 - 1.83: 90 Bond restraints: 9741 Sorted by residual: bond pdb=" C ILE A 213 " pdb=" O ILE A 213 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.12e-02 7.97e+03 4.96e+01 bond pdb=" C ILE A 213 " pdb=" N VAL A 214 " ideal model delta sigma weight residual 1.334 1.270 0.064 1.25e-02 6.40e+03 2.61e+01 bond pdb=" CA LEU D 26 " pdb=" C LEU D 26 " ideal model delta sigma weight residual 1.520 1.465 0.055 1.12e-02 7.97e+03 2.40e+01 bond pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.23e-02 6.61e+03 1.74e+01 bond pdb=" C GLY A 212 " pdb=" N ILE A 213 " ideal model delta sigma weight residual 1.334 1.296 0.038 1.26e-02 6.30e+03 8.89e+00 ... (remaining 9736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 13057 2.50 - 5.00: 118 5.00 - 7.50: 16 7.50 - 10.01: 2 10.01 - 12.51: 1 Bond angle restraints: 13194 Sorted by residual: angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 110.53 117.67 -7.14 9.40e-01 1.13e+00 5.77e+01 angle pdb=" C ILE A 213 " pdb=" CA ILE A 213 " pdb=" CB ILE A 213 " ideal model delta sigma weight residual 112.02 102.48 9.54 1.31e+00 5.83e-01 5.30e+01 angle pdb=" CA GLY A 212 " pdb=" C GLY A 212 " pdb=" N ILE A 213 " ideal model delta sigma weight residual 117.04 122.26 -5.22 9.90e-01 1.02e+00 2.78e+01 angle pdb=" O GLY A 212 " pdb=" C GLY A 212 " pdb=" N ILE A 213 " ideal model delta sigma weight residual 122.19 117.13 5.06 9.60e-01 1.09e+00 2.78e+01 angle pdb=" C ALA D 35 " pdb=" CA ALA D 35 " pdb=" CB ALA D 35 " ideal model delta sigma weight residual 116.54 110.67 5.87 1.15e+00 7.56e-01 2.60e+01 ... (remaining 13189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4951 17.65 - 35.30: 610 35.30 - 52.95: 190 52.95 - 70.60: 36 70.60 - 88.26: 6 Dihedral angle restraints: 5793 sinusoidal: 2257 harmonic: 3536 Sorted by residual: dihedral pdb=" CA LEU D 55 " pdb=" C LEU D 55 " pdb=" N LYS D 56 " pdb=" CA LYS D 56 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASP A 74 " pdb=" C ASP A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 5790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1102 0.044 - 0.088: 297 0.088 - 0.131: 90 0.131 - 0.175: 4 0.175 - 0.219: 2 Chirality restraints: 1495 Sorted by residual: chirality pdb=" CG LEU D 26 " pdb=" CB LEU D 26 " pdb=" CD1 LEU D 26 " pdb=" CD2 LEU D 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1492 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 111 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.18e+00 pdb=" C ALA A 111 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA A 111 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 112 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO S 236 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 236 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.025 5.00e-02 4.00e+02 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2592 2.81 - 3.33: 8213 3.33 - 3.85: 15338 3.85 - 4.38: 18816 4.38 - 4.90: 32240 Nonbonded interactions: 77199 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" NH1 ARG A 77 " model vdw 2.284 3.120 nonbonded pdb=" N ASP B 333 " pdb=" OD1 ASP B 333 " model vdw 2.308 3.120 nonbonded pdb=" NZ LYS B 89 " pdb=" OD1 ASP C 20 " model vdw 2.309 3.120 nonbonded pdb=" OG SER A 71 " pdb=" OD1 ASP A 74 " model vdw 2.320 3.040 nonbonded pdb=" OE1 GLN A 66 " pdb=" OG SER A 312 " model vdw 2.330 3.040 ... (remaining 77194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.003 0.079 9741 Z= 0.210 Angle : 0.624 12.508 13194 Z= 0.372 Chirality : 0.043 0.219 1495 Planarity : 0.004 0.050 1666 Dihedral : 17.241 88.256 3493 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.48 % Allowed : 24.27 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1199 helix: 1.09 (0.27), residues: 384 sheet: 0.79 (0.30), residues: 298 loop : -1.25 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 57 HIS 0.004 0.001 HIS A 79 PHE 0.012 0.001 PHE B 151 TYR 0.028 0.001 TYR S 235 ARG 0.001 0.000 ARG C 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 1.124 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 215 GLU cc_start: 0.7489 (mp0) cc_final: 0.7193 (mm-30) REVERT: D 31 THR cc_start: 0.4658 (OUTLIER) cc_final: 0.4331 (t) REVERT: G 29 LYS cc_start: 0.8049 (mttp) cc_final: 0.7589 (mmmm) REVERT: S 235 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.5857 (t80) outliers start: 36 outliers final: 28 residues processed: 139 average time/residue: 1.3867 time to fit residues: 205.5908 Evaluate side-chains 132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9741 Z= 0.255 Angle : 0.589 8.242 13194 Z= 0.316 Chirality : 0.044 0.257 1495 Planarity : 0.004 0.051 1666 Dihedral : 7.013 55.078 1362 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.13 % Allowed : 21.47 % Favored : 73.40 % 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: 0.30 (0.24), residues: 1199 helix: 1.44 (0.27), residues: 389 sheet: 0.79 (0.30), residues: 298 loop : -1.16 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 79 PHE 0.014 0.002 PHE B 151 TYR 0.025 0.002 TYR S 235 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 1.067 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7400 (mmm-85) REVERT: A 226 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7622 (mp) REVERT: A 236 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6557 (mttm) REVERT: B 118 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7871 (p0) REVERT: B 217 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7959 (pmm) REVERT: B 234 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: C 5 LEU cc_start: 0.8070 (mt) cc_final: 0.7850 (mp) REVERT: S 11 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8320 (tt) REVERT: S 43 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7712 (mmmm) REVERT: S 235 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6424 (t80) outliers start: 53 outliers final: 24 residues processed: 151 average time/residue: 1.3707 time to fit residues: 220.4643 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 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 315 HIS C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN G 59 ASN S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9741 Z= 0.232 Angle : 0.574 8.317 13194 Z= 0.307 Chirality : 0.044 0.256 1495 Planarity : 0.004 0.048 1666 Dihedral : 6.126 56.239 1333 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.22 % Allowed : 21.37 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1199 helix: 1.51 (0.27), residues: 389 sheet: 0.76 (0.30), residues: 298 loop : -1.22 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 57 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 151 TYR 0.025 0.002 TYR S 235 ARG 0.003 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 1.132 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7428 (mmm-85) REVERT: A 226 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7492 (mp) REVERT: A 233 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8159 (mm-40) REVERT: A 236 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6559 (mmtp) REVERT: B 46 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7611 (mtp85) REVERT: B 118 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7898 (p0) REVERT: B 175 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: B 217 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7946 (pmm) REVERT: B 234 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: C 5 LEU cc_start: 0.8101 (mt) cc_final: 0.7844 (mp) REVERT: C 330 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6637 (mtmt) REVERT: S 11 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8308 (tt) REVERT: S 235 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6275 (t80) outliers start: 54 outliers final: 24 residues processed: 151 average time/residue: 1.4561 time to fit residues: 233.4242 Evaluate side-chains 142 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 95 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 315 HIS C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9741 Z= 0.253 Angle : 0.585 7.951 13194 Z= 0.314 Chirality : 0.044 0.266 1495 Planarity : 0.004 0.049 1666 Dihedral : 5.774 57.319 1324 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.74 % Allowed : 21.86 % Favored : 73.40 % 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 (0.24), residues: 1199 helix: 1.51 (0.27), residues: 390 sheet: 0.70 (0.29), residues: 302 loop : -1.25 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 79 PHE 0.015 0.002 PHE C 196 TYR 0.026 0.002 TYR S 235 ARG 0.003 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 1.229 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7456 (mmm-85) REVERT: A 226 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7487 (mp) REVERT: B 46 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7600 (mtp85) REVERT: B 118 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7804 (p0) REVERT: B 175 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: B 217 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7916 (pmm) REVERT: B 234 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: C 5 LEU cc_start: 0.8141 (mt) cc_final: 0.7859 (mp) REVERT: C 330 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6812 (mtmt) REVERT: S 11 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8312 (tt) REVERT: S 235 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6289 (t80) outliers start: 49 outliers final: 25 residues processed: 144 average time/residue: 1.4419 time to fit residues: 220.4686 Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9741 Z= 0.359 Angle : 0.645 9.433 13194 Z= 0.345 Chirality : 0.047 0.316 1495 Planarity : 0.005 0.046 1666 Dihedral : 6.068 59.120 1324 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.51 % Allowed : 20.99 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1199 helix: 1.23 (0.27), residues: 396 sheet: 0.59 (0.29), residues: 300 loop : -1.44 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 47 HIS 0.005 0.001 HIS A 79 PHE 0.018 0.002 PHE C 196 TYR 0.029 0.002 TYR S 235 ARG 0.004 0.000 ARG C 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 1.090 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7483 (mmm-85) REVERT: A 226 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7610 (mp) REVERT: B 22 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.5770 (mtm180) REVERT: B 46 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7609 (mtp85) REVERT: B 118 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7985 (p0) REVERT: B 175 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: B 217 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7903 (pmm) REVERT: B 234 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: C 5 LEU cc_start: 0.8237 (mt) cc_final: 0.7938 (mp) REVERT: C 330 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6954 (mtmt) REVERT: S 11 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8296 (tt) REVERT: S 235 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6711 (t80) outliers start: 57 outliers final: 31 residues processed: 152 average time/residue: 1.4165 time to fit residues: 229.1786 Evaluate side-chains 152 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 0.0570 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9741 Z= 0.197 Angle : 0.553 9.836 13194 Z= 0.297 Chirality : 0.043 0.241 1495 Planarity : 0.004 0.045 1666 Dihedral : 5.698 57.100 1324 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.06 % Allowed : 22.73 % Favored : 73.21 % 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: 0.30 (0.24), residues: 1199 helix: 1.58 (0.27), residues: 390 sheet: 0.83 (0.29), residues: 289 loop : -1.30 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 79 PHE 0.012 0.001 PHE C 196 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 1.088 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7433 (mmm-85) REVERT: A 230 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6690 (pptt) REVERT: A 236 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6523 (mmtp) REVERT: B 22 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.5739 (mtm180) REVERT: B 46 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7614 (mtp85) REVERT: B 118 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7936 (p0) REVERT: B 175 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: B 217 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7898 (pmm) REVERT: B 234 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: C 5 LEU cc_start: 0.8201 (mt) cc_final: 0.7912 (mp) REVERT: C 330 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6818 (mtmt) REVERT: S 11 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8310 (tt) REVERT: S 235 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.5992 (t80) outliers start: 42 outliers final: 20 residues processed: 143 average time/residue: 1.4899 time to fit residues: 226.3451 Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9741 Z= 0.170 Angle : 0.528 10.750 13194 Z= 0.283 Chirality : 0.042 0.213 1495 Planarity : 0.004 0.048 1666 Dihedral : 5.441 57.290 1323 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.77 % Allowed : 23.11 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1199 helix: 1.79 (0.27), residues: 391 sheet: 0.97 (0.30), residues: 291 loop : -1.23 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 57 HIS 0.003 0.001 HIS A 79 PHE 0.012 0.001 PHE C 189 TYR 0.020 0.001 TYR S 235 ARG 0.003 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.139 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7389 (mmm-85) REVERT: A 230 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6677 (pptt) REVERT: B 22 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5830 (mtm180) REVERT: B 46 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7620 (mtp85) REVERT: B 118 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7683 (p0) REVERT: B 175 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: B 217 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7897 (pmm) REVERT: B 234 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8623 (m-80) REVERT: C 5 LEU cc_start: 0.8164 (mt) cc_final: 0.7864 (mp) REVERT: C 319 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 330 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6770 (mtmt) REVERT: S 11 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8303 (tt) REVERT: S 235 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.5677 (t80) outliers start: 39 outliers final: 19 residues processed: 142 average time/residue: 1.4528 time to fit residues: 219.5212 Evaluate side-chains 139 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 56 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 17 GLN C 188 HIS D 22 ASN S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9741 Z= 0.177 Angle : 0.535 11.172 13194 Z= 0.285 Chirality : 0.042 0.216 1495 Planarity : 0.004 0.047 1666 Dihedral : 5.202 58.459 1320 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.16 % Allowed : 22.53 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1199 helix: 1.87 (0.27), residues: 390 sheet: 0.99 (0.29), residues: 291 loop : -1.25 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 79 PHE 0.012 0.001 PHE C 189 TYR 0.019 0.001 TYR S 235 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 1.110 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6699 (pptt) REVERT: B 22 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.5771 (mtm180) REVERT: B 46 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7627 (mtp85) REVERT: B 118 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7702 (p0) REVERT: B 175 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: B 217 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7891 (pmm) REVERT: B 234 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8616 (m-80) REVERT: C 5 LEU cc_start: 0.8167 (mt) cc_final: 0.7871 (mp) REVERT: C 319 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8264 (mm) REVERT: C 330 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6801 (mtmt) REVERT: S 11 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8305 (tt) REVERT: S 235 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.5666 (t80) outliers start: 43 outliers final: 22 residues processed: 141 average time/residue: 1.4492 time to fit residues: 216.9689 Evaluate side-chains 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9980 chunk 109 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 340 ASN C 188 HIS D 22 ASN S 183 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9741 Z= 0.138 Angle : 0.507 11.672 13194 Z= 0.270 Chirality : 0.041 0.179 1495 Planarity : 0.004 0.048 1666 Dihedral : 4.940 57.353 1318 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.61 % Allowed : 24.27 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1199 helix: 1.96 (0.27), residues: 392 sheet: 0.87 (0.29), residues: 299 loop : -1.18 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS D 17 PHE 0.011 0.001 PHE C 189 TYR 0.015 0.001 TYR S 235 ARG 0.004 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6449 (tm) REVERT: A 230 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6701 (pmtt) REVERT: B 22 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5848 (mtm180) REVERT: B 175 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: B 215 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7084 (mp0) REVERT: B 217 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7938 (pmm) REVERT: B 234 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8591 (m-80) REVERT: C 5 LEU cc_start: 0.8177 (mt) cc_final: 0.7891 (mp) REVERT: S 11 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8311 (tt) REVERT: S 13 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7917 (tp40) REVERT: S 235 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5619 (t80) outliers start: 27 outliers final: 13 residues processed: 129 average time/residue: 1.4773 time to fit residues: 203.6120 Evaluate side-chains 127 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 94 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 188 HIS D 22 ASN S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9741 Z= 0.255 Angle : 0.590 12.169 13194 Z= 0.312 Chirality : 0.044 0.251 1495 Planarity : 0.004 0.051 1666 Dihedral : 5.190 59.626 1316 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.22 % Allowed : 24.95 % 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: 0.40 (0.24), residues: 1199 helix: 1.67 (0.27), residues: 397 sheet: 0.85 (0.29), residues: 298 loop : -1.29 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 79 PHE 0.016 0.002 PHE C 196 TYR 0.022 0.002 TYR S 235 ARG 0.003 0.000 ARG C 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.5719 (mtm180) REVERT: B 175 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: B 217 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7903 (pmm) REVERT: B 234 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8639 (m-80) REVERT: C 5 LEU cc_start: 0.8186 (mt) cc_final: 0.7896 (mp) REVERT: S 11 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8315 (tt) REVERT: S 235 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6132 (t80) outliers start: 23 outliers final: 13 residues processed: 122 average time/residue: 1.5158 time to fit residues: 196.4167 Evaluate side-chains 122 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 188 HIS S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.151536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109710 restraints weight = 10631.093| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.36 r_work: 0.2801 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9741 Z= 0.177 Angle : 0.539 12.190 13194 Z= 0.286 Chirality : 0.042 0.215 1495 Planarity : 0.004 0.044 1666 Dihedral : 4.879 58.876 1314 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.32 % Allowed : 25.05 % Favored : 72.63 % 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: 0.55 (0.24), residues: 1199 helix: 1.87 (0.27), residues: 391 sheet: 0.98 (0.29), residues: 291 loop : -1.24 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 79 PHE 0.012 0.001 PHE C 189 TYR 0.020 0.001 TYR S 235 ARG 0.002 0.000 ARG C 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4148.62 seconds wall clock time: 74 minutes 55.63 seconds (4495.63 seconds total)