Starting phenix.real_space_refine on Tue Feb 13 15:39:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/02_2024/7u2k_26313_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 55 5.16 5 C 4317 2.51 5 N 1159 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6755 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2123 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 272} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1675 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'KZR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.02, per 1000 atoms: 0.60 Number of scatterers: 6755 At special positions: 0 Unit cell: (76.3488, 124.067, 111.053, 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 55 16.00 O 1224 8.00 N 1159 7.00 C 4317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " 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: 2.39 Conformation dependent library (CDL) restraints added in 1.5 seconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 9 sheets defined 42.2% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'B' and resid 6 through 23 removed outlier: 4.188A pdb=" N ALA B 11 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 15 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 18 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 42 removed outlier: 3.683A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'D' and resid 66 through 95 Processing helix chain 'D' and resid 102 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 136 through 170 removed outlier: 4.027A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.892A pdb=" N PHE D 178 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 205 removed outlier: 3.699A pdb=" N LYS D 185 " --> pdb=" O PRO D 181 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 229 through 240 removed outlier: 3.833A pdb=" N LYS D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 261 removed outlier: 3.789A pdb=" N TYR D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 269 through 304 removed outlier: 3.574A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 312 through 336 removed outlier: 4.118A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'A' and resid 9 through 32 removed outlier: 4.045A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.687A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 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 242 through 254 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.570A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) 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 308 Processing helix chain 'A' and resid 331 through 351 Processing sheet with id= A, first strand: chain 'B' and resid 71 through 74 removed outlier: 4.119A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.231A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.833A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.061A 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: 3.973A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.945A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.426A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.580A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 336 through 339 removed outlier: 3.615A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 206 through 210 removed outlier: 3.521A pdb=" N LYS D 209 " --> pdb=" O ASP D 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.754A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 855 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: 1.86 Time building geometry restraints manager: 2.60 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: 1083 1.31 - 1.43: 1859 1.43 - 1.56: 3867 1.56 - 1.68: 3 1.68 - 1.81: 77 Bond restraints: 6889 Sorted by residual: bond pdb=" C17 KZR D 401 " pdb=" N18 KZR D 401 " ideal model delta sigma weight residual 1.503 1.294 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C27 KZR D 401 " pdb=" N18 KZR D 401 " ideal model delta sigma weight residual 1.496 1.305 0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C19 KZR D 401 " pdb=" N18 KZR D 401 " ideal model delta sigma weight residual 1.473 1.342 0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.32e-02 5.74e+03 8.91e+00 bond pdb=" N LYS B 337 " pdb=" CA LYS B 337 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.21e-02 6.83e+03 8.11e+00 ... (remaining 6884 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.81: 93 105.81 - 112.88: 3810 112.88 - 119.95: 2313 119.95 - 127.02: 3072 127.02 - 134.09: 73 Bond angle restraints: 9361 Sorted by residual: angle pdb=" C LYS B 78 " pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " ideal model delta sigma weight residual 110.24 104.88 5.36 1.46e+00 4.69e-01 1.35e+01 angle pdb=" CA ILE B 80 " pdb=" C ILE B 80 " pdb=" O ILE B 80 " ideal model delta sigma weight residual 121.92 118.12 3.80 1.17e+00 7.31e-01 1.06e+01 angle pdb=" CA TYR B 145 " pdb=" C TYR B 145 " pdb=" O TYR B 145 " ideal model delta sigma weight residual 120.75 117.66 3.09 1.12e+00 7.97e-01 7.63e+00 angle pdb=" CA LYS B 337 " pdb=" C LYS B 337 " pdb=" O LYS B 337 " ideal model delta sigma weight residual 120.71 117.88 2.83 1.06e+00 8.90e-01 7.11e+00 angle pdb=" N THR B 143 " pdb=" CA THR B 143 " pdb=" C THR B 143 " ideal model delta sigma weight residual 114.04 110.88 3.16 1.24e+00 6.50e-01 6.49e+00 ... (remaining 9356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 3894 25.51 - 51.02: 154 51.02 - 76.53: 15 76.53 - 102.04: 8 102.04 - 127.55: 5 Dihedral angle restraints: 4076 sinusoidal: 1481 harmonic: 2595 Sorted by residual: dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 179.99 -86.99 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CA ALA B 28 " pdb=" C ALA B 28 " pdb=" N THR B 29 " pdb=" CA THR B 29 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" C05 KZR D 401 " pdb=" C06 KZR D 401 " pdb=" C07 KZR D 401 " pdb=" C08 KZR D 401 " ideal model delta sinusoidal sigma weight residual 155.92 -76.53 -127.55 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 4073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 885 0.057 - 0.114: 194 0.114 - 0.171: 23 0.171 - 0.228: 1 0.228 - 0.285: 2 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CA LYS B 78 " pdb=" N LYS B 78 " pdb=" C LYS B 78 " pdb=" CB LYS B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA TYR B 145 " pdb=" N TYR B 145 " pdb=" C TYR B 145 " pdb=" CB TYR B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 1102 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.015 2.00e-02 2.50e+03 1.30e-02 3.40e+00 pdb=" CG TYR B 105 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO C 49 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 332 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO D 333 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " 0.019 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 904 2.74 - 3.28: 6624 3.28 - 3.82: 10148 3.82 - 4.36: 12007 4.36 - 4.90: 21210 Nonbonded interactions: 50893 Sorted by model distance: nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.198 2.440 nonbonded pdb=" O PRO D 122 " pdb=" OG SER D 125 " model vdw 2.238 2.440 nonbonded pdb=" O ASN D 137 " pdb=" NZ LYS D 141 " model vdw 2.258 2.520 nonbonded pdb=" OD1 ASN B 16 " pdb=" NH2 ARG B 19 " model vdw 2.266 2.520 nonbonded pdb=" O THR B 29 " pdb=" N GLN B 32 " model vdw 2.267 2.520 ... (remaining 50888 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: 0.770 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: 3.120 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.620 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.010 0.209 6889 Z= 0.607 Angle : 0.763 6.912 9361 Z= 0.430 Chirality : 0.048 0.285 1105 Planarity : 0.004 0.036 1173 Dihedral : 15.073 127.547 2387 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.43 % Allowed : 0.72 % Favored : 98.85 % 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: -1.90 (0.27), residues: 877 helix: -0.20 (0.28), residues: 358 sheet: -1.86 (0.36), residues: 171 loop : -1.96 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.005 0.001 HIS B 62 PHE 0.022 0.002 PHE A 274 TYR 0.032 0.002 TYR B 105 ARG 0.019 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8356 (mpp80) cc_final: 0.8145 (mpp80) REVERT: A 21 ARG cc_start: 0.7943 (tmm-80) cc_final: 0.7640 (ttp80) REVERT: A 261 ASP cc_start: 0.8459 (t0) cc_final: 0.8242 (t0) REVERT: A 313 ARG cc_start: 0.7808 (ttm110) cc_final: 0.7575 (ttm110) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.2664 time to fit residues: 34.8078 Evaluate side-chains 92 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.0980 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 0.0030 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6889 Z= 0.160 Angle : 0.557 8.846 9361 Z= 0.291 Chirality : 0.041 0.205 1105 Planarity : 0.003 0.033 1173 Dihedral : 10.350 122.484 970 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.01 % Allowed : 5.76 % Favored : 93.24 % 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: -0.61 (0.29), residues: 877 helix: 1.16 (0.28), residues: 364 sheet: -1.23 (0.37), residues: 170 loop : -1.65 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.001 PHE D 178 TYR 0.010 0.001 TYR B 124 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.841 Fit side-chains REVERT: B 333 ASP cc_start: 0.8025 (t0) cc_final: 0.7712 (t0) REVERT: A 21 ARG cc_start: 0.7944 (tmm-80) cc_final: 0.7622 (ttp80) REVERT: A 261 ASP cc_start: 0.8414 (t0) cc_final: 0.8000 (t0) outliers start: 7 outliers final: 1 residues processed: 106 average time/residue: 0.2449 time to fit residues: 32.8111 Evaluate side-chains 98 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6889 Z= 0.412 Angle : 0.622 8.983 9361 Z= 0.323 Chirality : 0.044 0.180 1105 Planarity : 0.003 0.031 1173 Dihedral : 9.481 123.442 968 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.86 % Allowed : 9.50 % Favored : 89.64 % 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: -0.56 (0.29), residues: 877 helix: 1.25 (0.29), residues: 367 sheet: -1.36 (0.36), residues: 178 loop : -1.61 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 226 HIS 0.003 0.001 HIS B 62 PHE 0.017 0.002 PHE A 274 TYR 0.009 0.001 TYR D 149 ARG 0.008 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9284 (tppp) cc_final: 0.9028 (tptp) REVERT: A 21 ARG cc_start: 0.7938 (tmm-80) cc_final: 0.7640 (ttp80) REVERT: A 261 ASP cc_start: 0.8454 (t0) cc_final: 0.8032 (t0) outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.2564 time to fit residues: 30.9617 Evaluate side-chains 98 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 0.0030 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6889 Z= 0.163 Angle : 0.508 6.168 9361 Z= 0.265 Chirality : 0.040 0.170 1105 Planarity : 0.003 0.044 1173 Dihedral : 8.989 124.222 968 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.58 % Allowed : 11.22 % Favored : 88.20 % 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: -0.24 (0.29), residues: 877 helix: 1.65 (0.29), residues: 362 sheet: -1.13 (0.36), residues: 176 loop : -1.62 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 226 HIS 0.003 0.001 HIS A 188 PHE 0.019 0.001 PHE D 178 TYR 0.009 0.001 TYR D 149 ARG 0.009 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: B 259 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8241 (pt0) REVERT: A 21 ARG cc_start: 0.7911 (tmm-80) cc_final: 0.7638 (ttp80) REVERT: A 261 ASP cc_start: 0.8444 (t0) cc_final: 0.8057 (t0) outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 0.2593 time to fit residues: 33.0128 Evaluate side-chains 95 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6889 Z= 0.218 Angle : 0.521 6.456 9361 Z= 0.270 Chirality : 0.041 0.170 1105 Planarity : 0.003 0.041 1173 Dihedral : 8.913 122.008 968 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.01 % Allowed : 12.23 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.30), residues: 877 helix: 1.76 (0.29), residues: 362 sheet: -0.97 (0.36), residues: 183 loop : -1.57 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 226 HIS 0.003 0.001 HIS A 188 PHE 0.009 0.001 PHE A 274 TYR 0.009 0.001 TYR D 149 ARG 0.012 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: B 123 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8582 (mt) REVERT: B 259 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8274 (pt0) REVERT: B 333 ASP cc_start: 0.8012 (t0) cc_final: 0.7706 (t0) REVERT: A 21 ARG cc_start: 0.7910 (tmm-80) cc_final: 0.7647 (ttp80) REVERT: A 261 ASP cc_start: 0.8435 (t0) cc_final: 0.8025 (t0) outliers start: 7 outliers final: 2 residues processed: 99 average time/residue: 0.2344 time to fit residues: 29.3398 Evaluate side-chains 97 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6889 Z= 0.276 Angle : 0.548 6.203 9361 Z= 0.284 Chirality : 0.041 0.169 1105 Planarity : 0.003 0.044 1173 Dihedral : 8.955 120.193 968 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.44 % Allowed : 12.52 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.30), residues: 877 helix: 1.79 (0.29), residues: 362 sheet: -1.05 (0.35), residues: 188 loop : -1.51 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 226 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE A 274 TYR 0.010 0.001 TYR D 149 ARG 0.011 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.819 Fit side-chains REVERT: B 123 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 259 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: B 333 ASP cc_start: 0.8087 (t0) cc_final: 0.7767 (t0) REVERT: A 21 ARG cc_start: 0.7895 (tmm-80) cc_final: 0.7639 (ttp80) REVERT: A 261 ASP cc_start: 0.8434 (t0) cc_final: 0.8020 (t0) REVERT: A 313 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7486 (ttm110) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.2497 time to fit residues: 31.7012 Evaluate side-chains 102 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6889 Z= 0.308 Angle : 0.569 6.898 9361 Z= 0.297 Chirality : 0.042 0.167 1105 Planarity : 0.003 0.033 1173 Dihedral : 8.979 119.708 968 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.73 % Allowed : 13.09 % Favored : 85.18 % 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: -0.00 (0.30), residues: 877 helix: 1.93 (0.29), residues: 356 sheet: -1.01 (0.36), residues: 184 loop : -1.52 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE A 274 TYR 0.010 0.001 TYR D 149 ARG 0.008 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.873 Fit side-chains REVERT: B 123 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8605 (mt) REVERT: B 259 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8334 (pt0) REVERT: A 21 ARG cc_start: 0.7908 (tmm-80) cc_final: 0.7661 (ttp80) REVERT: A 261 ASP cc_start: 0.8446 (t0) cc_final: 0.8037 (t0) outliers start: 12 outliers final: 6 residues processed: 100 average time/residue: 0.2651 time to fit residues: 33.7477 Evaluate side-chains 102 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 47 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6889 Z= 0.240 Angle : 0.545 6.846 9361 Z= 0.283 Chirality : 0.041 0.163 1105 Planarity : 0.003 0.055 1173 Dihedral : 8.850 119.197 968 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.87 % Allowed : 13.24 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 877 helix: 2.01 (0.29), residues: 356 sheet: -0.96 (0.35), residues: 189 loop : -1.51 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS A 188 PHE 0.009 0.001 PHE B 241 TYR 0.010 0.001 TYR D 149 ARG 0.013 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.870 Fit side-chains REVERT: B 123 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8585 (mt) REVERT: B 259 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: B 333 ASP cc_start: 0.8066 (t0) cc_final: 0.7751 (t0) REVERT: D 153 THR cc_start: 0.8782 (m) cc_final: 0.8181 (p) REVERT: A 21 ARG cc_start: 0.7903 (tmm-80) cc_final: 0.7663 (ttp80) REVERT: A 261 ASP cc_start: 0.8445 (t0) cc_final: 0.8051 (t0) REVERT: A 313 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7451 (ttm110) outliers start: 13 outliers final: 9 residues processed: 107 average time/residue: 0.2387 time to fit residues: 32.3289 Evaluate side-chains 105 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 70 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6889 Z= 0.209 Angle : 0.544 8.519 9361 Z= 0.280 Chirality : 0.041 0.161 1105 Planarity : 0.003 0.049 1173 Dihedral : 8.709 118.418 968 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.44 % Allowed : 13.53 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.30), residues: 877 helix: 1.98 (0.29), residues: 362 sheet: -0.80 (0.36), residues: 185 loop : -1.48 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.007 0.001 PHE A 274 TYR 0.009 0.001 TYR D 149 ARG 0.012 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.833 Fit side-chains REVERT: B 8 ARG cc_start: 0.7906 (ptp-170) cc_final: 0.7615 (ptp-170) REVERT: B 259 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: B 333 ASP cc_start: 0.8044 (t0) cc_final: 0.7825 (t0) REVERT: C 22 GLU cc_start: 0.8138 (tt0) cc_final: 0.7628 (tt0) REVERT: D 153 THR cc_start: 0.8782 (m) cc_final: 0.8148 (p) REVERT: A 21 ARG cc_start: 0.7918 (tmm-80) cc_final: 0.7676 (ttp80) REVERT: A 261 ASP cc_start: 0.8418 (t0) cc_final: 0.8017 (t0) outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.2392 time to fit residues: 31.3085 Evaluate side-chains 104 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 150 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6889 Z= 0.185 Angle : 0.530 8.008 9361 Z= 0.273 Chirality : 0.040 0.158 1105 Planarity : 0.003 0.025 1173 Dihedral : 8.546 115.948 968 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.44 % Allowed : 13.96 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.30), residues: 877 helix: 2.14 (0.29), residues: 360 sheet: -0.66 (0.36), residues: 183 loop : -1.54 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.000 HIS A 188 PHE 0.007 0.001 PHE A 189 TYR 0.010 0.001 TYR D 149 ARG 0.003 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.824 Fit side-chains REVERT: B 259 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: B 333 ASP cc_start: 0.8007 (t0) cc_final: 0.7785 (t0) REVERT: C 22 GLU cc_start: 0.8113 (tt0) cc_final: 0.7598 (tt0) REVERT: D 153 THR cc_start: 0.8769 (m) cc_final: 0.8115 (p) REVERT: A 21 ARG cc_start: 0.7915 (tmm-80) cc_final: 0.7681 (ttp80) REVERT: A 261 ASP cc_start: 0.8400 (t0) cc_final: 0.7990 (t0) REVERT: A 313 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7675 (ttm110) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.2414 time to fit residues: 31.4873 Evaluate side-chains 100 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.069364 restraints weight = 13135.652| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.10 r_work: 0.2783 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6889 Z= 0.193 Angle : 0.535 7.879 9361 Z= 0.275 Chirality : 0.040 0.157 1105 Planarity : 0.003 0.025 1173 Dihedral : 8.481 114.616 968 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.44 % Allowed : 14.24 % Favored : 84.32 % 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: 0.32 (0.30), residues: 877 helix: 2.16 (0.29), residues: 360 sheet: -0.63 (0.36), residues: 190 loop : -1.51 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.000 HIS A 188 PHE 0.023 0.001 PHE D 178 TYR 0.010 0.001 TYR D 149 ARG 0.003 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.41 seconds wall clock time: 32 minutes 45.03 seconds (1965.03 seconds total)