Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 10:15:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/04_2023/7u2k_26313_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/04_2023/7u2k_26313.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/04_2023/7u2k_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_26313/04_2023/7u2k_26313_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/04_2023/7u2k_26313_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/04_2023/7u2k_26313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/04_2023/7u2k_26313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/04_2023/7u2k_26313_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2k_26313/04_2023/7u2k_26313_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 3.79, per 1000 atoms: 0.56 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 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: 0.66 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: 1.96 Time building geometry restraints manager: 2.44 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: 5 102.04 - 127.55: 5 Dihedral angle restraints: 4073 sinusoidal: 1478 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 4070 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: 0.580 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: 0.000 Extract box with map and model: 3.370 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.650 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- 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 : 14.698 127.547 2384 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 % 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 *********************** 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 : 0.777 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.2616 time to fit residues: 34.0279 Evaluate side-chains 92 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0619 time to fit residues: 1.0997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 0.8498 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 6889 Z= 0.162 Angle : 0.550 9.754 9361 Z= 0.291 Chirality : 0.041 0.148 1105 Planarity : 0.003 0.033 1173 Dihedral : 9.741 118.588 965 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.86 % 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: -0.64 (0.29), residues: 877 helix: 1.13 (0.28), residues: 364 sheet: -1.25 (0.37), residues: 170 loop : -1.66 (0.33), residues: 343 *********************** 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 109 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.858 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 106 average time/residue: 0.2487 time to fit residues: 33.4850 Evaluate side-chains 96 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0668 time to fit residues: 1.2160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 6889 Z= 0.346 Angle : 0.596 8.782 9361 Z= 0.312 Chirality : 0.042 0.143 1105 Planarity : 0.003 0.038 1173 Dihedral : 9.672 116.044 965 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.43 % 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: -0.53 (0.29), residues: 877 helix: 1.29 (0.29), residues: 367 sheet: -1.29 (0.36), residues: 181 loop : -1.64 (0.33), residues: 329 *********************** 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 97 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.802 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 96 average time/residue: 0.2627 time to fit residues: 31.7410 Evaluate side-chains 94 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0657 time to fit residues: 1.3168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 0.0270 chunk 37 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8844 ------------------------------------------------------------------------------- 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 A 213 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 6889 Z= 0.167 Angle : 0.513 7.698 9361 Z= 0.267 Chirality : 0.040 0.132 1105 Planarity : 0.003 0.031 1173 Dihedral : 9.341 114.144 965 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.86 % 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: 1.71 (0.29), residues: 362 sheet: -1.11 (0.36), residues: 179 loop : -1.56 (0.33), residues: 336 *********************** 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 107 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.870 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 106 average time/residue: 0.2407 time to fit residues: 32.5905 Evaluate side-chains 96 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0727 time to fit residues: 1.5435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6889 Z= 0.223 Angle : 0.528 8.883 9361 Z= 0.273 Chirality : 0.040 0.137 1105 Planarity : 0.003 0.030 1173 Dihedral : 9.305 114.708 965 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 877 helix: 1.80 (0.29), residues: 362 sheet: -1.00 (0.35), residues: 188 loop : -1.45 (0.34), residues: 327 *********************** 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 100 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.836 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 99 average time/residue: 0.2561 time to fit residues: 32.0050 Evaluate side-chains 95 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0651 time to fit residues: 1.3227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 6 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 6889 Z= 0.265 Angle : 0.554 9.795 9361 Z= 0.287 Chirality : 0.041 0.136 1105 Planarity : 0.003 0.029 1173 Dihedral : 9.287 113.792 965 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 1.15 % 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: 0.07 (0.30), residues: 877 helix: 1.86 (0.29), residues: 362 sheet: -0.94 (0.36), residues: 188 loop : -1.43 (0.35), residues: 327 *********************** 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 103 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.845 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.2629 time to fit residues: 33.5895 Evaluate side-chains 98 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2298 time to fit residues: 1.9881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 0.0570 chunk 83 optimal weight: 0.9990 chunk 52 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8491 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 6889 Z= 0.160 Angle : 0.519 8.597 9361 Z= 0.269 Chirality : 0.040 0.131 1105 Planarity : 0.003 0.029 1173 Dihedral : 9.086 113.469 965 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.30), residues: 877 helix: 2.20 (0.29), residues: 359 sheet: -0.60 (0.37), residues: 180 loop : -1.47 (0.34), residues: 338 *********************** 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 103 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.833 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 99 average time/residue: 0.2640 time to fit residues: 33.1684 Evaluate side-chains 93 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0734 time to fit residues: 1.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 0.0070 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 6889 Z= 0.168 Angle : 0.530 8.335 9361 Z= 0.273 Chirality : 0.040 0.131 1105 Planarity : 0.003 0.028 1173 Dihedral : 9.016 112.855 965 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.29 % 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: 0.34 (0.30), residues: 877 helix: 2.18 (0.29), residues: 353 sheet: -0.65 (0.36), residues: 193 loop : -1.42 (0.34), residues: 331 *********************** 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 93 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.810 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.2620 time to fit residues: 30.6534 Evaluate side-chains 91 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0836 time to fit residues: 1.2088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.0470 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.0270 chunk 73 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.1594 ------------------------------------------------------------------------------- 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 ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 6889 Z= 0.148 Angle : 0.514 7.701 9361 Z= 0.263 Chirality : 0.039 0.139 1105 Planarity : 0.003 0.029 1173 Dihedral : 8.843 111.243 965 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.00 % 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: 0.39 (0.29), residues: 877 helix: 2.24 (0.29), residues: 353 sheet: -0.43 (0.36), residues: 188 loop : -1.52 (0.32), residues: 336 *********************** 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 99 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.870 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2540 time to fit residues: 32.0702 Evaluate side-chains 91 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.0082 ------------------------------------------------------------------------------- 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 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6889 Z= 0.190 Angle : 0.538 8.297 9361 Z= 0.276 Chirality : 0.040 0.135 1105 Planarity : 0.003 0.027 1173 Dihedral : 8.894 108.973 965 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.14 % 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: 0.48 (0.30), residues: 877 helix: 2.32 (0.29), residues: 355 sheet: -0.60 (0.36), residues: 197 loop : -1.36 (0.33), residues: 325 ********************** 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 91 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2505 time to fit residues: 28.7845 Evaluate side-chains 89 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.102173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.071587 restraints weight = 13187.007| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.04 r_work: 0.2839 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3153 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= 0.162 Angle : 0.530 7.941 9361 Z= 0.273 Chirality : 0.040 0.134 1105 Planarity : 0.003 0.025 1173 Dihedral : 8.838 108.735 965 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.14 % 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: 0.52 (0.30), residues: 877 helix: 2.34 (0.29), residues: 356 sheet: -0.45 (0.36), residues: 193 loop : -1.43 (0.33), residues: 328 =============================================================================== Job complete usr+sys time: 1617.00 seconds wall clock time: 29 minutes 56.98 seconds (1796.98 seconds total)