Starting phenix.real_space_refine on Mon Apr 6 02:03:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j93_61251/04_2026/9j93_61251.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j93_61251/04_2026/9j93_61251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j93_61251/04_2026/9j93_61251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j93_61251/04_2026/9j93_61251.map" model { file = "/net/cci-nas-00/data/ceres_data/9j93_61251/04_2026/9j93_61251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j93_61251/04_2026/9j93_61251.cif" } resolution = 3.54 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= -0.002 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5772 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 6365 2.51 5 N 1794 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10138 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3028 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3026 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 3022 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 359} Conformer: "B" Number of residues, atoms: 373, 3022 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 359} bond proxies already assigned to first conformer: 3083 Chain: "H" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1085 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'CIS': 1, 'TRANS': 215} Unresolved non-hydrogen bonds: 434 Unresolved non-hydrogen angles: 651 Unresolved non-hydrogen dihedrals: 217 Planarities with less than four sites: {'UNK:plan-1': 217} Unresolved non-hydrogen planarities: 217 Chain: "L" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1080 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'CIS': 2, 'TRANS': 213} Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 648 Unresolved non-hydrogen dihedrals: 216 Planarities with less than four sites: {'UNK:plan-1': 216} Unresolved non-hydrogen planarities: 216 Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1765 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.44, per 1000 atoms: 0.24 Number of scatterers: 10138 At special positions: 0 Unit cell: (118.8, 92.4, 172.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1948 8.00 N 1794 7.00 C 6365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG E 1 " - " ASN B 351 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 345 " " NAG I 1 " - " ASN A 239 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 453.7 milliseconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2686 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 24 sheets defined 33.1% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 18 through 34 removed outlier: 3.795A pdb=" N ILE B 28 " --> pdb=" O PHE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.599A pdb=" N VAL B 59 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.820A pdb=" N SER B 88 " --> pdb=" O HIS B 84 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.548A pdb=" N LEU B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 158 removed outlier: 3.638A pdb=" N ALA B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.500A pdb=" N ARG B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 209 removed outlier: 3.834A pdb=" N ASN B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 removed outlier: 4.097A pdb=" N HIS B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 236' Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.819A pdb=" N LEU B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 298 removed outlier: 3.636A pdb=" N TYR B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.599A pdb=" N GLU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 28 removed outlier: 3.564A pdb=" N AARG A 25 " --> pdb=" O HIS A 21 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.640A pdb=" N LYS A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.614A pdb=" N LEU A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.823A pdb=" N ILE A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.539A pdb=" N LYS A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 removed outlier: 4.043A pdb=" N TYR A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.722A pdb=" N GLU A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 270 through 293 removed outlier: 3.586A pdb=" N LEU A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 291 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'H' and resid 131 through 136 Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.755A pdb=" N UNK L 83 " --> pdb=" O UNK L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 129 Processing helix chain 'L' and resid 184 through 191 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.905A pdb=" N LYS C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.560A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 8 removed outlier: 6.277A pdb=" N VAL B 7 " --> pdb=" O VAL B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.687A pdb=" N GLY B 10 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE B 74 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA4, first strand: chain 'B' and resid 216 through 217 removed outlier: 6.635A pdb=" N TYR B 217 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N PHE B 242 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL B 239 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 241 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET B 354 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR B 369 " --> pdb=" O MET B 354 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 356 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AA6, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.254A pdb=" N ILE A 7 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 66 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 67 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 90 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 126 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.675A pdb=" N LEU A 348 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR A 363 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 350 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 328 through 329 removed outlier: 3.666A pdb=" N PHE A 328 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 336 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.519A pdb=" N UNK H 80 " --> pdb=" O UNK H 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 18 through 19 removed outlier: 4.029A pdb=" N UNK H 18 " --> pdb=" O UNK H 84 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N UNK H 84 " --> pdb=" O UNK H 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 35 through 37 removed outlier: 3.714A pdb=" N UNK H 99 " --> pdb=" O UNK H 106 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N UNK H 106 " --> pdb=" O UNK H 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 47 through 48 removed outlier: 4.118A pdb=" N UNK H 95 " --> pdb=" O UNK H 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 126 through 127 removed outlier: 4.005A pdb=" N UNK H 148 " --> pdb=" O UNK H 180 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N UNK H 180 " --> pdb=" O UNK H 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 126 through 127 removed outlier: 4.005A pdb=" N UNK H 148 " --> pdb=" O UNK H 180 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N UNK H 180 " --> pdb=" O UNK H 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.635A pdb=" N UNK L 22 " --> pdb=" O UNK L 7 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK L 19 " --> pdb=" O UNK L 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.522A pdb=" N UNK L 11 " --> pdb=" O UNK L 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N UNK L 105 " --> pdb=" O UNK L 11 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNK L 13 " --> pdb=" O UNK L 105 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.854A pdb=" N UNK L 135 " --> pdb=" O UNK L 120 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N UNK L 132 " --> pdb=" O UNK L 183 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N UNK L 175 " --> pdb=" O UNK L 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 156 through 157 removed outlier: 4.031A pdb=" N UNK L 150 " --> pdb=" O UNK L 157 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 19 through 20 removed outlier: 4.004A pdb=" N LEU C 20 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.507A pdb=" N GLU C 50 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC6, first strand: chain 'C' and resid 172 through 176 removed outlier: 6.569A pdb=" N TYR C 224 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY C 239 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS C 226 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY C 237 " --> pdb=" O CYS C 226 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.88 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: 3113 1.33 - 1.46: 1719 1.46 - 1.58: 5437 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 10316 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" N ASP C 232 " pdb=" CA ASP C 232 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.30e+01 bond pdb=" N GLY C 237 " pdb=" CA GLY C 237 " ideal model delta sigma weight residual 1.446 1.477 -0.031 9.50e-03 1.11e+04 1.03e+01 bond pdb=" N GLU C 231 " pdb=" CA GLU C 231 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 9.14e+00 bond pdb=" N TYR C 224 " pdb=" CA TYR C 224 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.36e+00 ... (remaining 10311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 13579 1.85 - 3.71: 430 3.71 - 5.56: 48 5.56 - 7.41: 9 7.41 - 9.27: 4 Bond angle restraints: 14070 Sorted by residual: angle pdb=" N PHE C 29 " pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " ideal model delta sigma weight residual 111.65 103.88 7.77 1.40e+00 5.10e-01 3.08e+01 angle pdb=" N THR C 229 " pdb=" CA THR C 229 " pdb=" C THR C 229 " ideal model delta sigma weight residual 112.38 105.89 6.49 1.22e+00 6.72e-01 2.83e+01 angle pdb=" N TYR C 234 " pdb=" CA TYR C 234 " pdb=" C TYR C 234 " ideal model delta sigma weight residual 112.93 107.32 5.61 1.12e+00 7.97e-01 2.51e+01 angle pdb=" N ILE A 194 " pdb=" CA ILE A 194 " pdb=" C ILE A 194 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 angle pdb=" N ILE A 199 " pdb=" CA ILE A 199 " pdb=" C ILE A 199 " ideal model delta sigma weight residual 113.71 109.01 4.70 9.50e-01 1.11e+00 2.44e+01 ... (remaining 14065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.51: 5782 24.51 - 49.02: 430 49.02 - 73.54: 62 73.54 - 98.05: 15 98.05 - 122.56: 7 Dihedral angle restraints: 6296 sinusoidal: 2161 harmonic: 4135 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 131.01 -38.01 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " pdb=" C5 NAG D 2 " ideal model delta sinusoidal sigma weight residual -62.96 59.60 -122.56 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" CA ARG C 206 " pdb=" C ARG C 206 " pdb=" N THR C 207 " pdb=" CA THR C 207 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1288 0.048 - 0.095: 293 0.095 - 0.143: 79 0.143 - 0.190: 3 0.190 - 0.238: 1 Chirality restraints: 1664 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 8.05e-01 chirality pdb=" CA VAL A 232 " pdb=" N VAL A 232 " pdb=" C VAL A 232 " pdb=" CB VAL A 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 1661 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 314 " -0.051 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO B 315 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 196 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C VAL C 196 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL C 196 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO C 197 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 29 " -0.002 2.00e-02 2.50e+03 1.37e-02 3.26e+00 pdb=" CG PHE C 29 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE C 29 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE C 29 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 29 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE C 29 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 29 " 0.001 2.00e-02 2.50e+03 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 98 2.62 - 3.19: 8556 3.19 - 3.76: 13724 3.76 - 4.33: 17998 4.33 - 4.90: 30472 Nonbonded interactions: 70848 Sorted by model distance: nonbonded pdb=" ND2 ASN A 231 " pdb=" O5 NAG A 901 " model vdw 2.046 3.120 nonbonded pdb=" OD1 ASP A 242 " pdb=" N THR A 243 " model vdw 2.064 3.120 nonbonded pdb=" ND2 ASN A 231 " pdb=" C1 NAG A 901 " model vdw 2.169 3.550 nonbonded pdb=" OE2 GLU B 20 " pdb=" OG1 THR B 277 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 144 " pdb=" OE1 GLN A 141 " model vdw 2.220 3.040 ... (remaining 70843 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = (chain 'H' and resid 3 through 218) selection = chain 'L' } 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=0.50 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 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 0.073 10328 Z= 0.214 Angle : 0.781 9.266 14103 Z= 0.411 Chirality : 0.043 0.238 1664 Planarity : 0.004 0.074 1848 Dihedral : 17.735 122.560 3601 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 27.68 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.24 (0.25), residues: 974 helix: -2.12 (0.28), residues: 265 sheet: -2.46 (0.39), residues: 172 loop : -2.03 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.012 0.001 TYR C 108 PHE 0.024 0.002 PHE C 29 TRP 0.013 0.001 TRP C 36 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00411 (10316) covalent geometry : angle 0.76844 (14070) SS BOND : bond 0.00501 ( 3) SS BOND : angle 0.94580 ( 6) hydrogen bonds : bond 0.32789 ( 296) hydrogen bonds : angle 10.16516 ( 814) link_BETA1-4 : bond 0.01100 ( 5) link_BETA1-4 : angle 3.13069 ( 15) link_NAG-ASN : bond 0.00364 ( 4) link_NAG-ASN : angle 3.48383 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.283 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1003 time to fit residues: 10.4947 Evaluate side-chains 73 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN B 170 ASN A 2 ASN A 101 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.187023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155620 restraints weight = 14097.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.154872 restraints weight = 19257.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.156127 restraints weight = 17676.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155728 restraints weight = 11766.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.156526 restraints weight = 11607.134| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 10328 Z= 0.376 Angle : 0.952 9.950 14103 Z= 0.467 Chirality : 0.052 0.305 1664 Planarity : 0.006 0.053 1848 Dihedral : 10.536 112.402 1735 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 6.36 % Allowed : 23.32 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.58 (0.24), residues: 974 helix: -1.78 (0.29), residues: 278 sheet: -3.03 (0.35), residues: 185 loop : -2.45 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 298 TYR 0.025 0.003 TYR A 208 PHE 0.037 0.004 PHE B 224 TRP 0.024 0.003 TRP C 33 HIS 0.008 0.002 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00903 (10316) covalent geometry : angle 0.93676 (14070) SS BOND : bond 0.00462 ( 3) SS BOND : angle 1.26979 ( 6) hydrogen bonds : bond 0.07121 ( 296) hydrogen bonds : angle 6.62932 ( 814) link_BETA1-4 : bond 0.01205 ( 5) link_BETA1-4 : angle 3.59902 ( 15) link_NAG-ASN : bond 0.00681 ( 4) link_NAG-ASN : angle 4.38719 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 77 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 170 ASN cc_start: 0.6527 (m-40) cc_final: 0.6153 (m-40) REVERT: A 315 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.5875 (mp10) REVERT: A 331 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7432 (tt) REVERT: C 79 LEU cc_start: 0.8093 (mt) cc_final: 0.7104 (mt) REVERT: C 156 SER cc_start: 0.6657 (OUTLIER) cc_final: 0.6252 (p) REVERT: C 187 PHE cc_start: 0.5588 (OUTLIER) cc_final: 0.4997 (t80) REVERT: C 209 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.6196 (m-80) outliers start: 54 outliers final: 26 residues processed: 125 average time/residue: 0.0796 time to fit residues: 14.8228 Evaluate side-chains 103 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 212 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 135 optimal weight: 0.0060 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.191978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163858 restraints weight = 13980.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.163173 restraints weight = 21550.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.164370 restraints weight = 19544.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164128 restraints weight = 12453.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.164794 restraints weight = 12581.765| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10328 Z= 0.138 Angle : 0.675 10.035 14103 Z= 0.327 Chirality : 0.041 0.235 1664 Planarity : 0.004 0.044 1848 Dihedral : 9.045 112.768 1735 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.94 % Allowed : 25.91 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.90 (0.25), residues: 974 helix: -1.06 (0.31), residues: 270 sheet: -2.48 (0.38), residues: 177 loop : -2.21 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.017 0.002 TYR C 108 PHE 0.043 0.002 PHE C 29 TRP 0.012 0.001 TRP C 33 HIS 0.003 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00313 (10316) covalent geometry : angle 0.66139 (14070) SS BOND : bond 0.00118 ( 3) SS BOND : angle 0.90815 ( 6) hydrogen bonds : bond 0.04703 ( 296) hydrogen bonds : angle 5.41114 ( 814) link_BETA1-4 : bond 0.01028 ( 5) link_BETA1-4 : angle 2.86732 ( 15) link_NAG-ASN : bond 0.00371 ( 4) link_NAG-ASN : angle 3.48830 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: B 170 ASN cc_start: 0.6483 (m-40) cc_final: 0.6081 (m-40) REVERT: A 181 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7977 (mt) REVERT: C 79 LEU cc_start: 0.7648 (mt) cc_final: 0.6612 (mt) outliers start: 25 outliers final: 18 residues processed: 98 average time/residue: 0.0804 time to fit residues: 11.7830 Evaluate side-chains 91 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 212 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 134 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN B 234 HIS C 151 GLN ** C 228 GLN ** 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 = 0.4222 r_free = 0.4222 target = 0.185588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154435 restraints weight = 14164.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153414 restraints weight = 19893.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154647 restraints weight = 17724.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155430 restraints weight = 12131.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155552 restraints weight = 12118.814| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 10328 Z= 0.319 Angle : 0.880 10.103 14103 Z= 0.427 Chirality : 0.048 0.257 1664 Planarity : 0.005 0.050 1848 Dihedral : 8.611 113.374 1735 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 6.95 % Allowed : 23.32 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.39 (0.24), residues: 974 helix: -1.39 (0.30), residues: 277 sheet: -2.89 (0.36), residues: 178 loop : -2.51 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.023 0.003 TYR A 208 PHE 0.039 0.003 PHE C 29 TRP 0.030 0.003 TRP C 33 HIS 0.007 0.002 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00772 (10316) covalent geometry : angle 0.86396 (14070) SS BOND : bond 0.00408 ( 3) SS BOND : angle 1.06214 ( 6) hydrogen bonds : bond 0.06113 ( 296) hydrogen bonds : angle 5.78192 ( 814) link_BETA1-4 : bond 0.01396 ( 5) link_BETA1-4 : angle 3.49577 ( 15) link_NAG-ASN : bond 0.00479 ( 4) link_NAG-ASN : angle 4.26187 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 75 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8056 (mt) REVERT: A 249 MET cc_start: 0.6348 (tmm) cc_final: 0.6087 (ttp) REVERT: A 292 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.5722 (mp10) REVERT: A 315 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6542 (mp-120) REVERT: A 331 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7604 (tt) outliers start: 59 outliers final: 35 residues processed: 123 average time/residue: 0.0870 time to fit residues: 15.5525 Evaluate side-chains 109 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 229 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 25 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 HIS ** C 228 GLN ** 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 = 0.4205 r_free = 0.4205 target = 0.183880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.152794 restraints weight = 14125.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152751 restraints weight = 19488.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154259 restraints weight = 18224.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.153952 restraints weight = 11373.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154706 restraints weight = 11444.887| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 10328 Z= 0.332 Angle : 0.898 10.234 14103 Z= 0.436 Chirality : 0.050 0.269 1664 Planarity : 0.005 0.047 1848 Dihedral : 8.536 112.752 1735 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 6.71 % Allowed : 25.09 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.70 (0.24), residues: 974 helix: -1.59 (0.29), residues: 277 sheet: -3.13 (0.33), residues: 185 loop : -2.71 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 258 TYR 0.024 0.003 TYR A 208 PHE 0.031 0.003 PHE B 224 TRP 0.025 0.002 TRP C 33 HIS 0.008 0.002 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00800 (10316) covalent geometry : angle 0.88269 (14070) SS BOND : bond 0.00480 ( 3) SS BOND : angle 1.19665 ( 6) hydrogen bonds : bond 0.05967 ( 296) hydrogen bonds : angle 5.84957 ( 814) link_BETA1-4 : bond 0.01241 ( 5) link_BETA1-4 : angle 3.55231 ( 15) link_NAG-ASN : bond 0.00307 ( 4) link_NAG-ASN : angle 4.32534 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 77 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7797 (tmm) cc_final: 0.6973 (ttt) REVERT: A 125 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6883 (mt0) REVERT: A 181 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8274 (mt) REVERT: A 249 MET cc_start: 0.6308 (tmm) cc_final: 0.6043 (ttp) REVERT: A 292 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.5863 (mp10) REVERT: A 315 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6416 (mp-120) REVERT: A 331 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7569 (tt) REVERT: C 82 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6241 (tt0) REVERT: C 209 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5873 (m-10) REVERT: C 241 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7818 (tmtt) outliers start: 57 outliers final: 39 residues processed: 126 average time/residue: 0.0816 time to fit residues: 15.1017 Evaluate side-chains 113 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 67 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 229 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 92 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 0.0870 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 122 optimal weight: 0.0060 chunk 54 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 HIS ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.190396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159579 restraints weight = 14181.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159281 restraints weight = 18626.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.160981 restraints weight = 17061.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.160827 restraints weight = 10594.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.161999 restraints weight = 11137.172| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10328 Z= 0.123 Angle : 0.663 9.863 14103 Z= 0.321 Chirality : 0.040 0.258 1664 Planarity : 0.004 0.045 1848 Dihedral : 7.767 111.798 1735 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.42 % Allowed : 28.62 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.00 (0.25), residues: 974 helix: -0.87 (0.31), residues: 270 sheet: -2.60 (0.36), residues: 175 loop : -2.42 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 348 TYR 0.018 0.002 TYR C 108 PHE 0.043 0.001 PHE C 29 TRP 0.012 0.001 TRP C 33 HIS 0.003 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00277 (10316) covalent geometry : angle 0.64746 (14070) SS BOND : bond 0.00079 ( 3) SS BOND : angle 0.87046 ( 6) hydrogen bonds : bond 0.03935 ( 296) hydrogen bonds : angle 4.96930 ( 814) link_BETA1-4 : bond 0.01066 ( 5) link_BETA1-4 : angle 2.99940 ( 15) link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 3.66940 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.5831 (mp10) REVERT: C 79 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7286 (mt) REVERT: C 175 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5074 (tt0) outliers start: 29 outliers final: 20 residues processed: 98 average time/residue: 0.0932 time to fit residues: 13.1301 Evaluate side-chains 91 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 212 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 30 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN ** A 231 ASN ** 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 = 0.4275 r_free = 0.4275 target = 0.190865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160201 restraints weight = 13979.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.159752 restraints weight = 18969.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.161317 restraints weight = 16713.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161051 restraints weight = 10937.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.161969 restraints weight = 10738.513| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10328 Z= 0.135 Angle : 0.667 11.015 14103 Z= 0.319 Chirality : 0.040 0.259 1664 Planarity : 0.004 0.077 1848 Dihedral : 7.562 111.832 1735 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.00 % Allowed : 28.15 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.80 (0.25), residues: 974 helix: -0.65 (0.31), residues: 270 sheet: -2.39 (0.38), residues: 175 loop : -2.36 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 100 TYR 0.013 0.001 TYR C 174 PHE 0.041 0.001 PHE C 29 TRP 0.013 0.001 TRP C 109 HIS 0.010 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00316 (10316) covalent geometry : angle 0.65205 (14070) SS BOND : bond 0.00070 ( 3) SS BOND : angle 0.93438 ( 6) hydrogen bonds : bond 0.03911 ( 296) hydrogen bonds : angle 4.77013 ( 814) link_BETA1-4 : bond 0.01123 ( 5) link_BETA1-4 : angle 3.03010 ( 15) link_NAG-ASN : bond 0.00288 ( 4) link_NAG-ASN : angle 3.61103 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9062 (t) REVERT: A 125 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6706 (tt0) REVERT: A 292 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6151 (mp10) REVERT: A 315 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6244 (mp-120) REVERT: C 79 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7285 (mt) outliers start: 34 outliers final: 25 residues processed: 97 average time/residue: 0.0845 time to fit residues: 11.9912 Evaluate side-chains 94 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 212 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 30 optimal weight: 0.0370 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 20.0000 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.191638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160730 restraints weight = 13906.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159864 restraints weight = 18840.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.161639 restraints weight = 16455.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.160979 restraints weight = 10949.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.162106 restraints weight = 11151.545| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10328 Z= 0.130 Angle : 0.656 11.124 14103 Z= 0.315 Chirality : 0.040 0.258 1664 Planarity : 0.004 0.064 1848 Dihedral : 7.448 111.468 1735 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.12 % Allowed : 28.15 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.63 (0.26), residues: 974 helix: -0.44 (0.32), residues: 269 sheet: -2.28 (0.39), residues: 175 loop : -2.31 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.013 0.001 TYR C 174 PHE 0.042 0.001 PHE C 29 TRP 0.015 0.001 TRP C 109 HIS 0.006 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00303 (10316) covalent geometry : angle 0.64133 (14070) SS BOND : bond 0.00047 ( 3) SS BOND : angle 0.89029 ( 6) hydrogen bonds : bond 0.03723 ( 296) hydrogen bonds : angle 4.65295 ( 814) link_BETA1-4 : bond 0.01106 ( 5) link_BETA1-4 : angle 2.94800 ( 15) link_NAG-ASN : bond 0.00309 ( 4) link_NAG-ASN : angle 3.55554 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9058 (t) REVERT: A 125 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6665 (tt0) REVERT: A 292 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6130 (mp10) REVERT: C 79 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7268 (mt) REVERT: C 82 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: C 241 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7814 (tmtt) outliers start: 35 outliers final: 26 residues processed: 98 average time/residue: 0.0881 time to fit residues: 12.7002 Evaluate side-chains 96 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 212 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 95 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 113 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 73 optimal weight: 0.0030 chunk 125 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.0570 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.192026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.160221 restraints weight = 13932.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.158964 restraints weight = 17042.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161112 restraints weight = 15227.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.161229 restraints weight = 9604.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161790 restraints weight = 10041.884| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10328 Z= 0.113 Angle : 0.628 11.025 14103 Z= 0.302 Chirality : 0.039 0.255 1664 Planarity : 0.004 0.055 1848 Dihedral : 7.167 110.576 1735 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.53 % Allowed : 28.39 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.39 (0.26), residues: 974 helix: -0.11 (0.32), residues: 269 sheet: -2.20 (0.39), residues: 179 loop : -2.20 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 246 TYR 0.013 0.001 TYR C 174 PHE 0.040 0.001 PHE C 29 TRP 0.013 0.001 TRP C 109 HIS 0.004 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00261 (10316) covalent geometry : angle 0.61453 (14070) SS BOND : bond 0.00039 ( 3) SS BOND : angle 0.76683 ( 6) hydrogen bonds : bond 0.03241 ( 296) hydrogen bonds : angle 4.36100 ( 814) link_BETA1-4 : bond 0.01089 ( 5) link_BETA1-4 : angle 2.81460 ( 15) link_NAG-ASN : bond 0.00385 ( 4) link_NAG-ASN : angle 3.31107 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 GLU cc_start: 0.5591 (pm20) cc_final: 0.5361 (pm20) REVERT: A 33 GLU cc_start: 0.5215 (mp0) cc_final: 0.5001 (mp0) REVERT: A 75 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.9048 (t) REVERT: A 125 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6507 (mt0) REVERT: A 198 ILE cc_start: 0.3778 (OUTLIER) cc_final: 0.3355 (tp) REVERT: A 249 MET cc_start: 0.6192 (tmm) cc_final: 0.5927 (ttp) REVERT: A 292 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6026 (mp10) REVERT: C 79 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6906 (mt) REVERT: C 241 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7630 (tmtt) outliers start: 30 outliers final: 22 residues processed: 98 average time/residue: 0.0933 time to fit residues: 13.5047 Evaluate side-chains 96 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6078 > 50: distance: 58 - 64: 4.031 distance: 64 - 65: 9.278 distance: 65 - 66: 3.940 distance: 65 - 68: 13.484 distance: 66 - 67: 29.449 distance: 66 - 75: 8.987 distance: 68 - 69: 7.467 distance: 69 - 70: 7.223 distance: 69 - 71: 4.297 distance: 70 - 72: 11.563 distance: 71 - 73: 8.474 distance: 73 - 74: 8.980 distance: 75 - 76: 10.102 distance: 76 - 77: 35.790 distance: 76 - 79: 18.512 distance: 77 - 78: 17.740 distance: 77 - 83: 7.000 distance: 79 - 80: 4.691 distance: 80 - 81: 29.078 distance: 80 - 82: 13.838 distance: 83 - 84: 18.848 distance: 84 - 85: 10.629 distance: 84 - 87: 10.385 distance: 85 - 86: 30.634 distance: 85 - 88: 13.254 distance: 88 - 89: 9.461 distance: 89 - 90: 4.513 distance: 89 - 92: 4.368 distance: 90 - 91: 9.989 distance: 90 - 94: 10.864 distance: 92 - 93: 20.157 distance: 94 - 95: 11.178 distance: 95 - 96: 6.146 distance: 95 - 98: 10.088 distance: 98 - 99: 8.608 distance: 99 - 100: 12.426 distance: 100 - 101: 3.560 distance: 101 - 102: 12.285 distance: 103 - 104: 14.370 distance: 104 - 105: 15.550 distance: 104 - 107: 11.853 distance: 105 - 106: 30.927 distance: 105 - 111: 18.613 distance: 107 - 108: 7.988 distance: 108 - 109: 17.127 distance: 108 - 110: 24.685 distance: 111 - 112: 13.810 distance: 112 - 113: 6.826 distance: 112 - 115: 18.072 distance: 113 - 114: 13.815 distance: 113 - 120: 13.194 distance: 115 - 116: 22.791 distance: 116 - 117: 8.347 distance: 117 - 118: 12.671 distance: 117 - 119: 14.952 distance: 120 - 121: 19.285 distance: 121 - 122: 8.627 distance: 121 - 124: 35.721 distance: 122 - 123: 17.901 distance: 122 - 126: 22.446 distance: 124 - 125: 14.195 distance: 126 - 127: 15.080 distance: 127 - 128: 8.983 distance: 128 - 129: 8.789 distance: 128 - 130: 16.323 distance: 130 - 131: 9.382 distance: 131 - 132: 5.378 distance: 131 - 134: 7.053 distance: 132 - 133: 9.120 distance: 132 - 137: 22.222 distance: 134 - 135: 20.806 distance: 134 - 136: 31.986