Starting phenix.real_space_refine on Thu Jun 4 20:52:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8za9_39875/06_2026/8za9_39875.cif Found real_map, /net/cci-nas-00/data/ceres_data/8za9_39875/06_2026/8za9_39875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8za9_39875/06_2026/8za9_39875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8za9_39875/06_2026/8za9_39875.map" model { file = "/net/cci-nas-00/data/ceres_data/8za9_39875/06_2026/8za9_39875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8za9_39875/06_2026/8za9_39875.cif" } resolution = 3.7 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 78 5.16 5 C 9767 2.51 5 N 2690 2.21 5 O 2861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15398 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3791 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 21, 'TRANS': 453} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3927 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 3901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3901 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 461} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3764 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 21, 'TRANS': 454} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.66, per 1000 atoms: 0.24 Number of scatterers: 15398 At special positions: 0 Unit cell: (102.343, 163.75, 252.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 2 15.00 O 2861 8.00 N 2690 7.00 C 9767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 219 " - pdb=" SG CYS G 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS G 237 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 791.8 milliseconds 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3618 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 30 sheets defined 19.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.741A pdb=" N ARG C 59 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.936A pdb=" N SER C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 291 removed outlier: 4.323A pdb=" N ALA C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.829A pdb=" N TRP C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.804A pdb=" N ASN E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.879A pdb=" N PHE E 212 " --> pdb=" O PRO E 209 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET E 213 " --> pdb=" O GLU E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 213' Processing helix chain 'E' and resid 217 through 292 removed outlier: 3.912A pdb=" N VAL E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Proline residue: E 224 - end of helix Proline residue: E 233 - end of helix removed outlier: 3.514A pdb=" N GLU E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 265 " --> pdb=" O THR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 391 Processing helix chain 'E' and resid 429 through 431 No H-bonds generated for 'chain 'E' and resid 429 through 431' Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.500A pdb=" N ASN G 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 213 removed outlier: 3.585A pdb=" N PHE G 212 " --> pdb=" O PRO G 209 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET G 213 " --> pdb=" O GLU G 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 209 through 213' Processing helix chain 'G' and resid 221 through 253 removed outlier: 3.856A pdb=" N ILE G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE G 232 " --> pdb=" O VAL G 228 " (cutoff:3.500A) Proline residue: G 233 - end of helix removed outlier: 4.102A pdb=" N LYS G 243 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU G 244 " --> pdb=" O TRP G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 294 removed outlier: 3.565A pdb=" N GLU G 268 " --> pdb=" O ILE G 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 215 through 290 Proline residue: D 228 - end of helix Processing helix chain 'D' and resid 299 through 304 removed outlier: 3.664A pdb=" N TRP D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 399 Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 14 removed outlier: 5.882A pdb=" N ILE C 11 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ALA C 115 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA C 13 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 108 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 97 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 112 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 93 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C 36 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 49 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP C 38 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 68 through 69 removed outlier: 3.794A pdb=" N ARG C 83 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.872A pdb=" N VAL C 166 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 162 removed outlier: 5.903A pdb=" N TYR C 173 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY C 141 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET C 181 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 128 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS C 134 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 121 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.771A pdb=" N ARG C 194 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 189 through 190 removed outlier: 5.927A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 126 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 133 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS D 137 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AA8, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.594A pdb=" N GLY C 381 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 420 " --> pdb=" O THR C 414 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.818A pdb=" N ILE E 11 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA E 115 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA E 13 " --> pdb=" O ALA E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 23 removed outlier: 3.677A pdb=" N THR E 19 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 84 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER E 79 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYS E 73 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 81 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 54 through 56 removed outlier: 3.504A pdb=" N LYS E 51 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL E 49 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 39 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG E 96 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS E 97 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA E 108 " --> pdb=" O CYS E 97 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE E 99 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP E 106 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 122 through 129 removed outlier: 6.447A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N HIS E 128 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY E 132 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 175 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 141 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE E 173 " --> pdb=" O GLY E 141 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 176 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 164 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 162 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 122 through 129 removed outlier: 6.447A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N HIS E 128 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY E 132 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 133 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 157 through 158 removed outlier: 4.148A pdb=" N TRP E 150 " --> pdb=" O ALA E 158 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET E 189 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 206 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS E 191 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 204 " --> pdb=" O CYS E 191 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 313 through 315 removed outlier: 3.516A pdb=" N VAL E 322 " --> pdb=" O ILE E 469 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU E 297 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU G 297 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP G 360 " --> pdb=" O VAL G 424 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL G 433 " --> pdb=" O THR G 446 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR G 446 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE G 435 " --> pdb=" O ILE G 444 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 443 through 447 removed outlier: 6.700A pdb=" N PHE E 435 " --> pdb=" O ILE E 444 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR E 446 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL E 433 " --> pdb=" O THR E 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER E 434 " --> pdb=" O PHE E 425 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU E 297 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU G 297 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE G 469 " --> pdb=" O VAL G 322 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 346 through 348 removed outlier: 4.077A pdb=" N TRP E 370 " --> pdb=" O MET E 398 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.568A pdb=" N VAL G 5 " --> pdb=" O HIS G 24 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS G 24 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR G 19 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE G 84 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS G 23 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL G 80 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.839A pdb=" N ALA G 13 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP G 106 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE G 99 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA G 108 " --> pdb=" O CYS G 97 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS G 97 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 112 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY G 93 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG G 96 " --> pdb=" O PHE G 39 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 39 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR G 98 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 51 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 122 through 129 removed outlier: 6.469A pdb=" N ARG G 134 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS G 128 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY G 132 " --> pdb=" O HIS G 128 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 179 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS G 137 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR G 177 " --> pdb=" O CYS G 137 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY G 141 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE G 173 " --> pdb=" O GLY G 141 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS G 162 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 147 through 151 removed outlier: 3.786A pdb=" N LEU G 147 " --> pdb=" O ASN G 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN G 194 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET G 189 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE G 206 " --> pdb=" O MET G 189 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER G 204 " --> pdb=" O CYS G 191 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE G 193 " --> pdb=" O LYS G 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS G 202 " --> pdb=" O ILE G 193 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 346 through 348 removed outlier: 4.153A pdb=" N TRP G 370 " --> pdb=" O MET G 398 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU G 397 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG G 404 " --> pdb=" O GLU G 397 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS G 399 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.642A pdb=" N SER D 3 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE D 26 " --> pdb=" O SER D 3 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.026A pdb=" N ILE D 11 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA D 115 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA D 13 " --> pdb=" O ALA D 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 54 through 56 removed outlier: 3.905A pdb=" N LYS D 54 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL D 46 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER D 40 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 108 " --> pdb=" O CYS D 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 166 through 167 removed outlier: 4.056A pdb=" N VAL D 166 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 174 " --> pdb=" O VAL D 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 332 through 333 removed outlier: 3.651A pdb=" N THR D 480 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP D 368 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 442 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS D 454 " --> pdb=" O PHE D 444 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 420 through 421 removed outlier: 4.131A pdb=" N THR D 420 " --> pdb=" O THR D 414 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR D 403 " --> pdb=" O LEU D 415 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 381 " --> pdb=" O VAL D 468 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4746 1.33 - 1.46: 2459 1.46 - 1.58: 8428 1.58 - 1.70: 6 1.70 - 1.82: 114 Bond restraints: 15753 Sorted by residual: bond pdb=" C27 H6P C 501 " pdb=" C30 H6P C 501 " ideal model delta sigma weight residual 1.334 1.524 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" CB PRO D 310 " pdb=" CG PRO D 310 " ideal model delta sigma weight residual 1.492 1.628 -0.136 5.00e-02 4.00e+02 7.35e+00 bond pdb=" O16 H6P C 501 " pdb=" P17 H6P C 501 " ideal model delta sigma weight residual 1.697 1.645 0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" O16 H6P C 501 " pdb=" P13 H6P C 501 " ideal model delta sigma weight residual 1.594 1.644 -0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" CB PRO E 335 " pdb=" CG PRO E 335 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.68e+00 ... (remaining 15748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 21177 3.24 - 6.49: 151 6.49 - 9.73: 21 9.73 - 12.97: 3 12.97 - 16.22: 3 Bond angle restraints: 21355 Sorted by residual: angle pdb=" CA PRO D 310 " pdb=" N PRO D 310 " pdb=" CD PRO D 310 " ideal model delta sigma weight residual 112.00 98.77 13.23 1.40e+00 5.10e-01 8.93e+01 angle pdb=" C LEU D 43 " pdb=" N ARG D 44 " pdb=" CA ARG D 44 " ideal model delta sigma weight residual 121.70 133.05 -11.35 1.80e+00 3.09e-01 3.98e+01 angle pdb=" C LEU C 43 " pdb=" N ARG C 44 " pdb=" CA ARG C 44 " ideal model delta sigma weight residual 121.70 132.41 -10.71 1.80e+00 3.09e-01 3.54e+01 angle pdb=" C28 H6P C 501 " pdb=" C27 H6P C 501 " pdb=" C30 H6P C 501 " ideal model delta sigma weight residual 127.23 111.01 16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" C21 H6P C 501 " pdb=" C30 H6P C 501 " pdb=" C27 H6P C 501 " ideal model delta sigma weight residual 125.58 109.69 15.89 3.00e+00 1.11e-01 2.81e+01 ... (remaining 21350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 9200 34.16 - 68.32: 320 68.32 - 102.48: 13 102.48 - 136.65: 0 136.65 - 170.81: 2 Dihedral angle restraints: 9535 sinusoidal: 3921 harmonic: 5614 Sorted by residual: dihedral pdb=" CB CYS E 219 " pdb=" SG CYS E 219 " pdb=" SG CYS G 219 " pdb=" CB CYS G 219 " ideal model delta sinusoidal sigma weight residual 93.00 11.24 81.76 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CA ARG E 293 " pdb=" C ARG E 293 " pdb=" N ARG E 294 " pdb=" CA ARG E 294 " ideal model delta harmonic sigma weight residual 180.00 -139.56 -40.44 0 5.00e+00 4.00e-02 6.54e+01 dihedral pdb=" CA ARG E 294 " pdb=" C ARG E 294 " pdb=" N THR E 295 " pdb=" CA THR E 295 " ideal model delta harmonic sigma weight residual 180.00 146.45 33.55 0 5.00e+00 4.00e-02 4.50e+01 ... (remaining 9532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1415 0.030 - 0.061: 544 0.061 - 0.091: 199 0.091 - 0.121: 166 0.121 - 0.151: 15 Chirality restraints: 2339 Sorted by residual: chirality pdb=" CA LYS E 246 " pdb=" N LYS E 246 " pdb=" C LYS E 246 " pdb=" CB LYS E 246 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE D 471 " pdb=" N ILE D 471 " pdb=" C ILE D 471 " pdb=" CB ILE D 471 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA PRO E 306 " pdb=" N PRO E 306 " pdb=" C PRO E 306 " pdb=" CB PRO E 306 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 2336 not shown) Planarity restraints: 2765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 H6P C 501 " -0.076 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C27 H6P C 501 " -0.533 2.00e-02 2.50e+03 pdb=" C28 H6P C 501 " 0.267 2.00e-02 2.50e+03 pdb=" C30 H6P C 501 " 0.296 2.00e-02 2.50e+03 pdb=" C31 H6P C 501 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 309 " -0.088 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO D 310 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO D 310 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 310 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 305 " 0.051 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO E 306 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 306 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 306 " 0.041 5.00e-02 4.00e+02 ... (remaining 2762 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 512 2.70 - 3.25: 14643 3.25 - 3.80: 24477 3.80 - 4.35: 29759 4.35 - 4.90: 50129 Nonbonded interactions: 119520 Sorted by model distance: nonbonded pdb=" OG SER C 462 " pdb=" OE1 GLU C 463 " model vdw 2.152 3.040 nonbonded pdb=" O ASP E 307 " pdb=" ND2 ASN E 337 " model vdw 2.218 3.120 nonbonded pdb=" O TRP C 378 " pdb=" ND1 HIS C 379 " model vdw 2.220 3.120 nonbonded pdb=" O PRO G 414 " pdb=" NZ LYS G 416 " model vdw 2.226 3.120 nonbonded pdb=" O SER G 378 " pdb=" OG SER G 378 " model vdw 2.233 3.040 ... (remaining 119515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 209 or (resid 210 and (name N or \ name CA or name C or name O or name CB )) or resid 211 through 213 or (resid 21 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 215 through \ 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or re \ sid 219 through 299 or (resid 300 and (name N or name CA or name C or name O or \ name CB )) or resid 301 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 484)) selection = (chain 'D' and (resid 1 through 211 or (resid 212 through 214 and (name N or nam \ e CA or name C or name O or name CB )) or resid 215 through 484)) } ncs_group { reference = (chain 'E' and (resid 1 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 323 or (resid 324 a \ nd (name N or name CA or name C or name O or name CB )) or resid 325 through 396 \ or (resid 397 and (name N or name CA or name C or name O or name CB )) or resid \ 398 through 492)) selection = (chain 'G' and (resid 1 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 492)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4166 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 : 0.004 0.190 15763 Z= 0.187 Angle : 0.758 16.217 21375 Z= 0.422 Chirality : 0.044 0.151 2339 Planarity : 0.008 0.300 2765 Dihedral : 16.533 170.807 5887 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.14 % Favored : 95.65 % Rotamer: Outliers : 0.36 % Allowed : 27.71 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1933 helix: 2.70 (0.30), residues: 297 sheet: -0.19 (0.23), residues: 544 loop : -1.03 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 461 TYR 0.044 0.001 TYR E 239 PHE 0.010 0.001 PHE D 434 TRP 0.050 0.002 TRP D 392 HIS 0.005 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (15753) covalent geometry : angle 0.75864 / 0.42 (21355) SS BOND : bond 0.00204 / 0.10 ( 10) SS BOND : angle 0.38946 / 0.27 ( 20) hydrogen bonds : bond 0.22395 / 14.90 ( 556) hydrogen bonds : angle 8.73711 / 5.98 ( 1542) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 ARG cc_start: 0.3537 (ttm170) cc_final: 0.2959 (tpt90) REVERT: E 315 LEU cc_start: 0.7173 (tp) cc_final: 0.6921 (tt) REVERT: G 133 ILE cc_start: 0.7276 (mt) cc_final: 0.6793 (mm) REVERT: G 271 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8494 (ptpp) REVERT: G 361 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6027 (mt-10) REVERT: D 269 MET cc_start: 0.5829 (mmp) cc_final: 0.5448 (mmm) outliers start: 6 outliers final: 1 residues processed: 219 average time/residue: 0.1697 time to fit residues: 51.1934 Evaluate side-chains 116 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 257 PHE Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN E 391 ASN G 128 HIS ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 HIS ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.128803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.117842 restraints weight = 71055.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.118989 restraints weight = 115788.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.119397 restraints weight = 58072.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.119475 restraints weight = 44026.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.119588 restraints weight = 39013.480| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15763 Z= 0.148 Angle : 0.634 9.409 21375 Z= 0.332 Chirality : 0.045 0.169 2339 Planarity : 0.005 0.067 2765 Dihedral : 6.936 149.753 2148 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.76 % Rotamer: Outliers : 4.25 % Allowed : 24.48 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1933 helix: 2.87 (0.29), residues: 297 sheet: -0.15 (0.23), residues: 560 loop : -0.94 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 296 TYR 0.035 0.002 TYR E 239 PHE 0.019 0.001 PHE E 212 TRP 0.023 0.001 TRP D 392 HIS 0.009 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (15753) covalent geometry : angle 0.63455 / 0.33 (21355) SS BOND : bond 0.00284 / 0.14 ( 10) SS BOND : angle 0.45628 / 0.28 ( 20) hydrogen bonds : bond 0.04441 / 2.88 ( 556) hydrogen bonds : angle 6.24560 / 4.27 ( 1542) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 124 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 480 THR cc_start: 0.4956 (OUTLIER) cc_final: 0.4629 (m) REVERT: E 416 LYS cc_start: 0.5825 (OUTLIER) cc_final: 0.5489 (ptpp) REVERT: D 258 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7458 (pp20) REVERT: D 390 LYS cc_start: 0.1103 (OUTLIER) cc_final: 0.0432 (mttt) outliers start: 71 outliers final: 18 residues processed: 181 average time/residue: 0.1289 time to fit residues: 34.6349 Evaluate side-chains 119 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 348 ARG Chi-restraints excluded: chain D residue 390 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 0.0570 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 HIS ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 HIS E 391 ASN G 92 ASN ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 145 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.122425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.113662 restraints weight = 67994.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.112883 restraints weight = 111759.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.112198 restraints weight = 65883.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.112314 restraints weight = 51235.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.112352 restraints weight = 39855.557| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 15763 Z= 0.309 Angle : 0.822 10.122 21375 Z= 0.430 Chirality : 0.049 0.189 2339 Planarity : 0.007 0.069 2765 Dihedral : 7.802 153.703 2142 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.98 % Favored : 92.81 % Rotamer: Outliers : 6.52 % Allowed : 22.92 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 1933 helix: 2.26 (0.29), residues: 300 sheet: -1.00 (0.21), residues: 584 loop : -1.07 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 262 TYR 0.033 0.003 TYR E 436 PHE 0.035 0.003 PHE G 327 TRP 0.017 0.002 TRP G 394 HIS 0.008 0.002 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.31 (15753) covalent geometry : angle 0.82134 / 0.43 (21355) SS BOND : bond 0.00542 / 0.26 ( 10) SS BOND : angle 1.24952 / 0.75 ( 20) hydrogen bonds : bond 0.05092 / 3.27 ( 556) hydrogen bonds : angle 6.80184 / 4.64 ( 1542) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 97 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.1053 (OUTLIER) cc_final: -0.0709 (tp30) REVERT: C 379 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6209 (m90) REVERT: E 125 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.6206 (mpp) REVERT: E 193 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8608 (mm) REVERT: E 244 LEU cc_start: 0.4210 (OUTLIER) cc_final: 0.3918 (tp) REVERT: E 416 LYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5834 (ptpp) REVERT: G 61 MET cc_start: 0.4639 (mmm) cc_final: 0.3849 (mmt) REVERT: G 445 TYR cc_start: 0.6792 (t80) cc_final: 0.6583 (t80) REVERT: D 258 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7501 (pp20) REVERT: D 262 ARG cc_start: 0.6203 (tmm160) cc_final: 0.5910 (ttp-110) REVERT: D 367 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.4543 (p90) REVERT: D 477 THR cc_start: 0.1955 (m) cc_final: 0.1541 (p) outliers start: 109 outliers final: 54 residues processed: 192 average time/residue: 0.1301 time to fit residues: 37.1844 Evaluate side-chains 143 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 82 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 379 HIS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 492 ARG Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 348 ARG Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 472 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 5 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 189 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.0670 chunk 32 optimal weight: 10.0000 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.125091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.117170 restraints weight = 72059.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.115879 restraints weight = 83381.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.115135 restraints weight = 62262.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.115218 restraints weight = 64384.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.115067 restraints weight = 49660.494| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15763 Z= 0.123 Angle : 0.617 10.337 21375 Z= 0.315 Chirality : 0.045 0.233 2339 Planarity : 0.005 0.059 2765 Dihedral : 7.142 153.736 2142 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.09 % Favored : 95.71 % Rotamer: Outliers : 4.19 % Allowed : 24.96 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 1933 helix: 2.78 (0.29), residues: 295 sheet: -0.89 (0.21), residues: 580 loop : -0.94 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 320 TYR 0.013 0.001 TYR G 64 PHE 0.038 0.002 PHE G 393 TRP 0.018 0.001 TRP C 266 HIS 0.005 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15753) covalent geometry : angle 0.61694 / 0.32 (21355) SS BOND : bond 0.00316 / 0.15 ( 10) SS BOND : angle 0.51984 / 0.31 ( 20) hydrogen bonds : bond 0.03959 / 2.58 ( 556) hydrogen bonds : angle 5.99173 / 4.10 ( 1542) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 95 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.0940 (OUTLIER) cc_final: -0.1149 (mm-30) REVERT: C 379 HIS cc_start: 0.7014 (OUTLIER) cc_final: 0.6387 (m-70) REVERT: C 480 THR cc_start: 0.4598 (OUTLIER) cc_final: 0.4341 (m) REVERT: E 193 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8733 (mm) REVERT: E 416 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5585 (ptpp) REVERT: G 61 MET cc_start: 0.5050 (mmm) cc_final: 0.4657 (mmm) REVERT: G 105 TYR cc_start: 0.4848 (OUTLIER) cc_final: 0.4575 (m-80) REVERT: G 266 LEU cc_start: 0.8112 (pp) cc_final: 0.7747 (mm) REVERT: G 361 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6550 (mt-10) REVERT: D 262 ARG cc_start: 0.5887 (tmm160) cc_final: 0.5530 (ttp-110) REVERT: D 367 TYR cc_start: 0.5792 (OUTLIER) cc_final: 0.4545 (p90) REVERT: D 477 THR cc_start: 0.2032 (m) cc_final: 0.1744 (p) outliers start: 70 outliers final: 29 residues processed: 154 average time/residue: 0.1312 time to fit residues: 30.3486 Evaluate side-chains 121 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 379 HIS Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 348 ARG Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 395 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 90 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 HIS ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN E 399 HIS ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.112004 restraints weight = 65941.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.112238 restraints weight = 107428.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.111918 restraints weight = 52413.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.112131 restraints weight = 41351.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.112622 restraints weight = 34579.217| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 15763 Z= 0.292 Angle : 0.777 13.753 21375 Z= 0.405 Chirality : 0.048 0.198 2339 Planarity : 0.007 0.068 2765 Dihedral : 7.543 137.511 2142 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.33 % Favored : 91.46 % Rotamer: Outliers : 5.69 % Allowed : 23.94 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1933 helix: 2.38 (0.28), residues: 300 sheet: -1.31 (0.21), residues: 580 loop : -1.22 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 320 TYR 0.033 0.003 TYR E 436 PHE 0.034 0.002 PHE G 327 TRP 0.018 0.002 TRP D 392 HIS 0.016 0.002 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.29 (15753) covalent geometry : angle 0.77687 / 0.40 (21355) SS BOND : bond 0.00525 / 0.24 ( 10) SS BOND : angle 1.23089 / 0.74 ( 20) hydrogen bonds : bond 0.04780 / 3.10 ( 556) hydrogen bonds : angle 6.55344 / 4.47 ( 1542) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 84 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.3701 (OUTLIER) cc_final: 0.3139 (mmm) REVERT: C 57 GLU cc_start: 0.0943 (OUTLIER) cc_final: -0.1584 (tm-30) REVERT: C 100 GLN cc_start: 0.4054 (OUTLIER) cc_final: 0.3718 (tt0) REVERT: E 188 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.6940 (p0) REVERT: E 193 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8492 (mm) REVERT: E 244 LEU cc_start: 0.3738 (OUTLIER) cc_final: 0.3533 (tt) REVERT: E 255 LYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5401 (mmtm) REVERT: E 416 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5909 (ptpp) REVERT: E 436 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: G 61 MET cc_start: 0.5009 (mmm) cc_final: 0.4657 (mmm) REVERT: G 213 MET cc_start: 0.4757 (OUTLIER) cc_final: 0.4540 (mmm) REVERT: G 231 MET cc_start: 0.5033 (mmp) cc_final: 0.4287 (mmt) REVERT: G 359 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7463 (p90) REVERT: G 361 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6822 (mt-10) REVERT: G 445 TYR cc_start: 0.7148 (t80) cc_final: 0.6729 (t80) REVERT: D 367 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.4891 (p90) REVERT: D 477 THR cc_start: 0.1612 (m) cc_final: 0.1220 (p) outliers start: 95 outliers final: 52 residues processed: 168 average time/residue: 0.1141 time to fit residues: 29.9577 Evaluate side-chains 145 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 81 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 255 LYS Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 399 HIS Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 359 TYR Chi-restraints excluded: chain G residue 380 GLU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 242 ASN ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.124067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.117561 restraints weight = 71191.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.114551 restraints weight = 55183.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.113480 restraints weight = 69458.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.113739 restraints weight = 61529.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.113579 restraints weight = 44505.943| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5676 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15763 Z= 0.123 Angle : 0.627 12.136 21375 Z= 0.319 Chirality : 0.045 0.206 2339 Planarity : 0.005 0.061 2765 Dihedral : 5.983 96.330 2142 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 3.53 % Allowed : 26.27 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 1933 helix: 2.75 (0.29), residues: 294 sheet: -1.15 (0.21), residues: 599 loop : -1.06 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 262 TYR 0.013 0.001 TYR G 64 PHE 0.023 0.001 PHE G 393 TRP 0.019 0.001 TRP C 266 HIS 0.014 0.001 HIS E 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (15753) covalent geometry : angle 0.62739 / 0.32 (21355) SS BOND : bond 0.00337 / 0.15 ( 10) SS BOND : angle 0.60649 / 0.36 ( 20) hydrogen bonds : bond 0.03836 / 2.53 ( 556) hydrogen bonds : angle 5.82846 / 3.97 ( 1542) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 87 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.3178 (OUTLIER) cc_final: 0.2735 (mmm) REVERT: C 57 GLU cc_start: 0.1236 (OUTLIER) cc_final: -0.1168 (mm-30) REVERT: E 193 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8801 (mm) REVERT: E 247 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.4518 (tt0) REVERT: E 255 LYS cc_start: 0.6209 (OUTLIER) cc_final: 0.5517 (mmtm) REVERT: E 416 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5874 (ptpp) REVERT: G 61 MET cc_start: 0.5405 (mmm) cc_final: 0.5159 (mmm) REVERT: G 105 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.4726 (m-80) REVERT: G 213 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.4237 (mmm) REVERT: G 231 MET cc_start: 0.4369 (mmp) cc_final: 0.3666 (mmt) REVERT: G 266 LEU cc_start: 0.8035 (pp) cc_final: 0.7777 (mm) REVERT: G 359 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7696 (p90) REVERT: G 398 MET cc_start: 0.7019 (mmm) cc_final: 0.6796 (tpt) REVERT: D 367 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.4756 (p90) outliers start: 59 outliers final: 36 residues processed: 135 average time/residue: 0.1141 time to fit residues: 24.1853 Evaluate side-chains 125 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 255 LYS Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 359 TYR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 367 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 119 optimal weight: 6.9990 chunk 115 optimal weight: 0.1980 chunk 3 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 0.0010 chunk 52 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 HIS ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.124589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.116428 restraints weight = 70489.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.114734 restraints weight = 77800.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.113448 restraints weight = 67508.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.113854 restraints weight = 67838.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.113765 restraints weight = 46029.655| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15763 Z= 0.110 Angle : 0.600 12.665 21375 Z= 0.305 Chirality : 0.045 0.203 2339 Planarity : 0.005 0.059 2765 Dihedral : 5.374 59.627 2142 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 3.53 % Allowed : 26.27 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 1933 helix: 2.82 (0.29), residues: 295 sheet: -1.02 (0.21), residues: 599 loop : -0.99 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 319 TYR 0.017 0.001 TYR G 403 PHE 0.021 0.001 PHE G 425 TRP 0.019 0.001 TRP C 266 HIS 0.005 0.001 HIS G 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (15753) covalent geometry : angle 0.60012 / 0.31 (21355) SS BOND : bond 0.00348 / 0.16 ( 10) SS BOND : angle 0.61335 / 0.36 ( 20) hydrogen bonds : bond 0.03655 / 2.41 ( 556) hydrogen bonds : angle 5.54556 / 3.78 ( 1542) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 80 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 PHE cc_start: 0.0098 (OUTLIER) cc_final: -0.0565 (p90) REVERT: C 14 MET cc_start: 0.3054 (OUTLIER) cc_final: 0.2814 (mmm) REVERT: C 57 GLU cc_start: 0.0890 (OUTLIER) cc_final: -0.1160 (mm-30) REVERT: E 125 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5579 (mtt) REVERT: E 193 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8728 (mm) REVERT: E 255 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.5191 (mmtm) REVERT: G 105 TYR cc_start: 0.5184 (OUTLIER) cc_final: 0.4815 (m-80) REVERT: G 231 MET cc_start: 0.4473 (mmp) cc_final: 0.3726 (mmt) REVERT: G 266 LEU cc_start: 0.8167 (pp) cc_final: 0.7933 (mm) REVERT: G 398 MET cc_start: 0.7044 (mmm) cc_final: 0.6758 (tpt) REVERT: D 262 ARG cc_start: 0.5865 (ttp80) cc_final: 0.5476 (ttp-110) REVERT: D 367 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.4710 (p90) REVERT: D 430 LYS cc_start: 0.7394 (mmtm) cc_final: 0.6328 (mmtt) outliers start: 59 outliers final: 38 residues processed: 129 average time/residue: 0.1119 time to fit residues: 23.1011 Evaluate side-chains 123 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 255 LYS Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 367 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN C 399 ASN ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 HIS ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.121055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.112424 restraints weight = 67776.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.111584 restraints weight = 115594.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.110808 restraints weight = 66387.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.110921 restraints weight = 55969.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.111175 restraints weight = 38588.904| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 15763 Z= 0.259 Angle : 0.743 12.632 21375 Z= 0.385 Chirality : 0.048 0.167 2339 Planarity : 0.006 0.062 2765 Dihedral : 6.008 49.491 2142 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.97 % Favored : 91.83 % Rotamer: Outliers : 4.67 % Allowed : 25.73 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1933 helix: 2.52 (0.28), residues: 300 sheet: -1.47 (0.21), residues: 591 loop : -1.20 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 77 TYR 0.036 0.003 TYR G 359 PHE 0.019 0.002 PHE G 393 TRP 0.019 0.002 TRP G 360 HIS 0.011 0.002 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 (15753) covalent geometry : angle 0.74204 / 0.38 (21355) SS BOND : bond 0.00523 / 0.24 ( 10) SS BOND : angle 1.17991 / 0.70 ( 20) hydrogen bonds : bond 0.04495 / 2.94 ( 556) hydrogen bonds : angle 6.23596 / 4.25 ( 1542) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 73 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 PHE cc_start: 0.0407 (OUTLIER) cc_final: -0.0420 (p90) REVERT: C 57 GLU cc_start: 0.1034 (OUTLIER) cc_final: -0.0862 (tp30) REVERT: E 193 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8558 (mm) REVERT: G 213 MET cc_start: 0.4985 (mmm) cc_final: 0.4477 (tpt) REVERT: G 359 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7331 (p90) REVERT: G 445 TYR cc_start: 0.7132 (t80) cc_final: 0.6558 (t80) REVERT: D 262 ARG cc_start: 0.6104 (ttp80) cc_final: 0.5699 (ttp-110) REVERT: D 367 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.4812 (p90) outliers start: 78 outliers final: 53 residues processed: 141 average time/residue: 0.1075 time to fit residues: 24.2356 Evaluate side-chains 128 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 70 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 TYR Chi-restraints excluded: chain G residue 359 TYR Chi-restraints excluded: chain G residue 380 GLU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 472 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 192 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN C 100 GLN C 289 GLN E 24 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 HIS ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.122157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.113649 restraints weight = 69779.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.111394 restraints weight = 75359.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.109855 restraints weight = 68630.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.110006 restraints weight = 65240.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.109793 restraints weight = 49078.497| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15763 Z= 0.156 Angle : 0.648 11.646 21375 Z= 0.331 Chirality : 0.046 0.175 2339 Planarity : 0.005 0.062 2765 Dihedral : 5.697 58.926 2142 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.64 % Favored : 94.21 % Rotamer: Outliers : 3.77 % Allowed : 26.45 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1933 helix: 2.65 (0.28), residues: 301 sheet: -1.44 (0.21), residues: 593 loop : -1.15 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 77 TYR 0.021 0.002 TYR C 105 PHE 0.018 0.001 PHE G 425 TRP 0.016 0.001 TRP C 266 HIS 0.008 0.001 HIS G 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (15753) covalent geometry : angle 0.64787 / 0.33 (21355) SS BOND : bond 0.00484 / 0.21 ( 10) SS BOND : angle 0.94150 / 0.54 ( 20) hydrogen bonds : bond 0.03911 / 2.59 ( 556) hydrogen bonds : angle 5.89271 / 4.01 ( 1542) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 72 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 PHE cc_start: 0.0317 (OUTLIER) cc_final: -0.0498 (p90) REVERT: C 57 GLU cc_start: 0.1742 (OUTLIER) cc_final: -0.0831 (tp30) REVERT: E 193 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8820 (mm) REVERT: G 213 MET cc_start: 0.4462 (mmm) cc_final: 0.4041 (tpt) REVERT: G 266 LEU cc_start: 0.8302 (pp) cc_final: 0.8029 (mm) REVERT: G 359 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7234 (p90) REVERT: G 398 MET cc_start: 0.6874 (mmm) cc_final: 0.6383 (tpt) REVERT: D 262 ARG cc_start: 0.5975 (ttp80) cc_final: 0.5641 (ttp-110) REVERT: D 367 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4525 (p90) outliers start: 63 outliers final: 54 residues processed: 127 average time/residue: 0.1014 time to fit residues: 21.2033 Evaluate side-chains 129 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 70 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 TYR Chi-restraints excluded: chain G residue 359 TYR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 380 GLU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 367 TYR Chi-restraints excluded: chain D residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 177 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 141 optimal weight: 0.2980 chunk 123 optimal weight: 0.8980 chunk 93 optimal weight: 0.0060 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.124143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.116336 restraints weight = 71289.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.114100 restraints weight = 78123.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.113450 restraints weight = 70895.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.113776 restraints weight = 64875.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.113758 restraints weight = 44638.156| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15763 Z= 0.113 Angle : 0.610 12.003 21375 Z= 0.308 Chirality : 0.045 0.185 2339 Planarity : 0.005 0.061 2765 Dihedral : 4.955 48.706 2142 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 2.93 % Allowed : 27.05 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 1933 helix: 2.93 (0.29), residues: 295 sheet: -1.17 (0.21), residues: 590 loop : -1.08 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 77 TYR 0.017 0.001 TYR G 64 PHE 0.023 0.001 PHE G 425 TRP 0.019 0.001 TRP C 266 HIS 0.004 0.001 HIS G 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15753) covalent geometry : angle 0.60996 / 0.31 (21355) SS BOND : bond 0.00358 / 0.16 ( 10) SS BOND : angle 0.91161 / 0.52 ( 20) hydrogen bonds : bond 0.03563 / 2.36 ( 556) hydrogen bonds : angle 5.46364 / 3.71 ( 1542) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 77 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 PHE cc_start: 0.0898 (OUTLIER) cc_final: 0.0069 (p90) REVERT: C 14 MET cc_start: 0.3008 (OUTLIER) cc_final: 0.2793 (mmm) REVERT: C 57 GLU cc_start: 0.0281 (OUTLIER) cc_final: -0.1223 (mm-30) REVERT: E 193 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8721 (mm) REVERT: G 266 LEU cc_start: 0.8117 (pp) cc_final: 0.7899 (mm) REVERT: G 398 MET cc_start: 0.6956 (mmm) cc_final: 0.6557 (tpt) REVERT: D 262 ARG cc_start: 0.5659 (ttp80) cc_final: 0.5449 (ttp-110) REVERT: D 367 TYR cc_start: 0.5812 (OUTLIER) cc_final: 0.4487 (p90) REVERT: D 430 LYS cc_start: 0.7449 (mmtm) cc_final: 0.6508 (mmtt) outliers start: 49 outliers final: 38 residues processed: 117 average time/residue: 0.1056 time to fit residues: 19.8020 Evaluate side-chains 115 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 72 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 367 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 96 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 189 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 0.0770 chunk 89 optimal weight: 0.2980 overall best weight: 0.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** 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 = 0.4542 r_free = 0.4542 target = 0.125090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.116738 restraints weight = 69303.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.115907 restraints weight = 84971.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.115533 restraints weight = 56046.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.115454 restraints weight = 53193.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.115208 restraints weight = 44624.393| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15763 Z= 0.106 Angle : 0.603 12.486 21375 Z= 0.302 Chirality : 0.045 0.186 2339 Planarity : 0.005 0.061 2765 Dihedral : 4.753 47.724 2142 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 2.57 % Allowed : 27.17 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1933 helix: 3.01 (0.28), residues: 296 sheet: -1.09 (0.21), residues: 595 loop : -0.98 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 77 TYR 0.017 0.001 TYR G 403 PHE 0.023 0.001 PHE G 425 TRP 0.019 0.001 TRP C 266 HIS 0.007 0.001 HIS G 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (15753) covalent geometry : angle 0.60339 / 0.30 (21355) SS BOND : bond 0.00344 / 0.16 ( 10) SS BOND : angle 0.51478 / 0.33 ( 20) hydrogen bonds : bond 0.03473 / 2.30 ( 556) hydrogen bonds : angle 5.28552 / 3.60 ( 1542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2768.25 seconds wall clock time: 48 minutes 47.52 seconds (2927.52 seconds total)