Starting phenix.real_space_refine on Wed Aug 5 09:32:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xno_67054/08_2026/9xno_67054.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xno_67054/08_2026/9xno_67054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xno_67054/08_2026/9xno_67054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xno_67054/08_2026/9xno_67054.map" model { file = "/net/cci-nas-00/data/ceres_data/9xno_67054/08_2026/9xno_67054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xno_67054/08_2026/9xno_67054.cif" } resolution = 2.93 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= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 29 5.16 5 C 5744 2.51 5 N 1585 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8998 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4425 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain: "D" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4509 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 554} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.19, per 1000 atoms: 0.24 Number of scatterers: 8998 At special positions: 0 Unit cell: (83.3, 94.35, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 6 15.00 Mg 2 11.99 O 1632 8.00 N 1585 7.00 C 5744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 351.2 milliseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 59.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.905A pdb=" N TYR C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 12' Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 22 through 50 removed outlier: 3.933A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.586A pdb=" N ALA C 63 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 89 " --> pdb=" O HIS C 85 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 removed outlier: 4.051A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 125 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 155 removed outlier: 5.101A pdb=" N SER C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Proline residue: C 140 - end of helix removed outlier: 3.610A pdb=" N PHE C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 159 through 176 removed outlier: 3.617A pdb=" N ALA C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 209 removed outlier: 3.933A pdb=" N ALA C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 220 through 268 removed outlier: 3.714A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR C 244 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.837A pdb=" N CYS C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 319 removed outlier: 3.732A pdb=" N LEU C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 443 through 453 removed outlier: 3.649A pdb=" N GLU C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.662A pdb=" N LEU C 458 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 460 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 492 removed outlier: 3.792A pdb=" N ILE C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 520 removed outlier: 4.089A pdb=" N GLU C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 516 " --> pdb=" O GLN C 512 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 Processing helix chain 'C' and resid 564 through 571 Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 21 removed outlier: 3.789A pdb=" N GLN D 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.974A pdb=" N ARG D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 54 removed outlier: 3.880A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 110 removed outlier: 3.932A pdb=" N PHE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.809A pdb=" N TRP D 122 " --> pdb=" O PRO D 118 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.859A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 159 removed outlier: 3.576A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.790A pdb=" N ALA D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 167 " --> pdb=" O TRP D 163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.736A pdb=" N ARG D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.727A pdb=" N LEU D 201 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 202 " --> pdb=" O ALA D 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 202' Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 211 through 217 removed outlier: 3.569A pdb=" N LEU D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 247 removed outlier: 4.077A pdb=" N GLU D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 273 removed outlier: 3.820A pdb=" N SER D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.634A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.635A pdb=" N GLY D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 removed outlier: 3.683A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 390 through 397 Processing helix chain 'D' and resid 438 through 444 removed outlier: 3.733A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.926A pdb=" N ALA D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 Processing helix chain 'D' and resid 473 through 477 removed outlier: 4.161A pdb=" N ASP D 476 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 500 removed outlier: 3.828A pdb=" N VAL D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 528 removed outlier: 3.734A pdb=" N MET D 525 " --> pdb=" O GLU D 521 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 571 Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 362 removed outlier: 6.926A pdb=" N LYS C 357 " --> pdb=" O GLN C 345 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN C 345 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE C 359 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU C 341 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU C 398 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP C 343 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 396 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 394 " --> pdb=" O GLN C 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 370 through 372 removed outlier: 6.706A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 549 " --> pdb=" O ASP C 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 417 through 419 removed outlier: 8.066A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 428 through 429 Processing sheet with id=AA5, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AA6, first strand: chain 'D' and resid 364 through 369 removed outlier: 5.081A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 426 through 427 removed outlier: 6.713A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA D 379 " --> pdb=" O MET D 539 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 552 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 380 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 563 " --> pdb=" O VAL D 555 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN D 557 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 407 through 408 378 hydrogen bonds defined for protein. 1107 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: 1.43 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2909 1.33 - 1.45: 1075 1.45 - 1.57: 5122 1.57 - 1.68: 8 1.68 - 1.80: 61 Bond restraints: 9175 Sorted by residual: bond pdb=" C3' ANP C 602 " pdb=" C4' ANP C 602 " ideal model delta sigma weight residual 1.532 1.264 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C3' ANP D 601 " pdb=" C4' ANP D 601 " ideal model delta sigma weight residual 1.532 1.264 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C4' ANP C 602 " pdb=" O4' ANP C 602 " ideal model delta sigma weight residual 1.431 1.688 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C4' ANP D 601 " pdb=" O4' ANP D 601 " ideal model delta sigma weight residual 1.431 1.687 -0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C3' ANP C 602 " pdb=" O3' ANP C 602 " ideal model delta sigma weight residual 1.386 1.503 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 9170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 12276 2.82 - 5.63: 160 5.63 - 8.45: 32 8.45 - 11.26: 8 11.26 - 14.08: 4 Bond angle restraints: 12480 Sorted by residual: angle pdb=" O3A ANP D 601 " pdb=" PA ANP D 601 " pdb=" O5' ANP D 601 " ideal model delta sigma weight residual 98.09 112.17 -14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O3A ANP C 602 " pdb=" PA ANP C 602 " pdb=" O5' ANP C 602 " ideal model delta sigma weight residual 98.09 112.12 -14.03 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O1A ANP D 601 " pdb=" PA ANP D 601 " pdb=" O2A ANP D 601 " ideal model delta sigma weight residual 120.18 108.79 11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O1A ANP C 602 " pdb=" PA ANP C 602 " pdb=" O2A ANP C 602 " ideal model delta sigma weight residual 120.18 108.81 11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O1B ANP C 602 " pdb=" PB ANP C 602 " pdb=" O2B ANP C 602 " ideal model delta sigma weight residual 120.08 109.11 10.97 3.00e+00 1.11e-01 1.34e+01 ... (remaining 12475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.03: 5232 27.03 - 54.06: 215 54.06 - 81.08: 51 81.08 - 108.11: 3 108.11 - 135.14: 2 Dihedral angle restraints: 5503 sinusoidal: 2193 harmonic: 3310 Sorted by residual: dihedral pdb=" CA LEU C 106 " pdb=" C LEU C 106 " pdb=" N SER C 107 " pdb=" CA SER C 107 " ideal model delta harmonic sigma weight residual -180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA THR C 525 " pdb=" C THR C 525 " pdb=" N VAL C 526 " pdb=" CA VAL C 526 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU D 396 " pdb=" C LEU D 396 " pdb=" N SER D 397 " pdb=" CA SER D 397 " ideal model delta harmonic sigma weight residual 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 5500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 945 0.045 - 0.091: 420 0.091 - 0.136: 77 0.136 - 0.181: 6 0.181 - 0.226: 1 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CA SER C 107 " pdb=" N SER C 107 " pdb=" C SER C 107 " pdb=" CB SER C 107 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE C 569 " pdb=" N PHE C 569 " pdb=" C PHE C 569 " pdb=" CB PHE C 569 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CG LEU D 365 " pdb=" CB LEU D 365 " pdb=" CD1 LEU D 365 " pdb=" CD2 LEU D 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1446 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 569 " 0.016 2.00e-02 2.50e+03 1.47e-02 3.79e+00 pdb=" CG PHE C 569 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE C 569 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 569 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 569 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 569 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 569 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 141 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO D 142 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 297 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO D 298 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 298 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 298 " 0.024 5.00e-02 4.00e+02 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 22 2.48 - 3.09: 5934 3.09 - 3.69: 12215 3.69 - 4.30: 18452 4.30 - 4.90: 32060 Nonbonded interactions: 68683 Sorted by model distance: nonbonded pdb=" O1G ANP D 601 " pdb="MG MG D 602 " model vdw 1.880 2.170 nonbonded pdb=" OG SER D 390 " pdb="MG MG D 602 " model vdw 1.935 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ANP C 602 " model vdw 1.990 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.085 2.170 nonbonded pdb=" OG SER C 476 " pdb=" OE1 GLU C 479 " model vdw 2.209 3.040 ... (remaining 68678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.160 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:9.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 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 : 0.011 0.268 9175 Z= 0.472 Angle : 0.910 14.076 12480 Z= 0.442 Chirality : 0.049 0.226 1449 Planarity : 0.005 0.048 1589 Dihedral : 15.847 135.137 3369 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.87 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.56 (0.19), residues: 1150 helix: -2.55 (0.16), residues: 676 sheet: -2.85 (0.67), residues: 40 loop : -3.67 (0.22), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 431 TYR 0.014 0.002 TYR C 134 PHE 0.034 0.002 PHE C 569 TRP 0.012 0.002 TRP D 163 HIS 0.006 0.001 HIS C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.01059 / 0.47 ( 9175) covalent geometry : angle 0.90953 / 0.44 (12480) hydrogen bonds : bond 0.13730 / 8.65 ( 378) hydrogen bonds : angle 5.90536 / 4.09 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.342 Fit side-chains REVERT: C 67 ARG cc_start: 0.6988 (mtp85) cc_final: 0.6337 (tmm160) REVERT: C 170 MET cc_start: 0.9002 (mtp) cc_final: 0.8788 (mtm) REVERT: C 183 ARG cc_start: 0.7390 (ptm-80) cc_final: 0.7055 (ptp90) REVERT: D 45 MET cc_start: 0.8263 (mtm) cc_final: 0.7878 (mtp) REVERT: D 306 ASP cc_start: 0.7966 (m-30) cc_final: 0.7702 (m-30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.8065 time to fit residues: 91.9296 Evaluate side-chains 67 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 GLN C 433 ASN D 16 GLN D 237 GLN D 370 ASN D 431 ASN D 492 GLN D 529 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104738 restraints weight = 12043.170| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.99 r_work: 0.3242 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9175 Z= 0.125 Angle : 0.589 7.597 12480 Z= 0.292 Chirality : 0.040 0.196 1449 Planarity : 0.004 0.035 1589 Dihedral : 10.604 136.648 1321 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.51 % Allowed : 11.33 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.14 (0.22), residues: 1150 helix: -1.41 (0.19), residues: 665 sheet: -2.30 (0.65), residues: 40 loop : -3.03 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 566 TYR 0.010 0.001 TYR C 114 PHE 0.021 0.001 PHE C 569 TRP 0.012 0.001 TRP D 163 HIS 0.005 0.001 HIS C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9175) covalent geometry : angle 0.58903 / 0.29 (12480) hydrogen bonds : bond 0.04641 / 3.04 ( 378) hydrogen bonds : angle 4.55783 / 3.26 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.237 Fit side-chains REVERT: C 67 ARG cc_start: 0.7246 (mtp85) cc_final: 0.6182 (tmm160) REVERT: C 81 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8176 (mmp-170) REVERT: C 183 ARG cc_start: 0.8026 (ptm-80) cc_final: 0.7303 (ptp90) REVERT: C 520 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7564 (mpp) REVERT: C 562 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6459 (ptt-90) REVERT: D 306 ASP cc_start: 0.8259 (m-30) cc_final: 0.8010 (m-30) REVERT: D 521 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8099 (tm-30) REVERT: D 566 ARG cc_start: 0.7088 (mtp-110) cc_final: 0.6627 (mtp85) outliers start: 14 outliers final: 2 residues processed: 85 average time/residue: 0.6107 time to fit residues: 54.7316 Evaluate side-chains 71 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 562 ARG Chi-restraints excluded: chain D residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.0370 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 191 ASN C 320 GLN C 330 GLN D 529 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107020 restraints weight = 11970.584| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.99 r_work: 0.3265 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9175 Z= 0.104 Angle : 0.524 6.635 12480 Z= 0.262 Chirality : 0.039 0.172 1449 Planarity : 0.003 0.034 1589 Dihedral : 8.513 125.353 1321 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.40 % Allowed : 13.05 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1150 helix: -0.77 (0.20), residues: 677 sheet: -2.40 (0.59), residues: 50 loop : -2.76 (0.25), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 566 TYR 0.009 0.001 TYR C 114 PHE 0.024 0.001 PHE C 569 TRP 0.009 0.001 TRP D 163 HIS 0.003 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 9175) covalent geometry : angle 0.52433 / 0.26 (12480) hydrogen bonds : bond 0.03936 / 2.58 ( 378) hydrogen bonds : angle 4.20859 / 3.02 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.264 Fit side-chains REVERT: C 67 ARG cc_start: 0.7356 (mtp85) cc_final: 0.6180 (tmm160) REVERT: C 107 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.7311 (t) REVERT: C 183 ARG cc_start: 0.8001 (ptm-80) cc_final: 0.7243 (ptp90) REVERT: C 235 GLU cc_start: 0.8089 (tp30) cc_final: 0.7850 (tp30) REVERT: C 520 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7483 (mpp) REVERT: C 562 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6507 (ptt-90) REVERT: D 306 ASP cc_start: 0.8232 (m-30) cc_final: 0.7978 (m-30) REVERT: D 521 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8003 (tm-30) REVERT: D 566 ARG cc_start: 0.7036 (mtp-110) cc_final: 0.6644 (mtp85) outliers start: 13 outliers final: 2 residues processed: 88 average time/residue: 0.6800 time to fit residues: 63.0610 Evaluate side-chains 76 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 562 ARG Chi-restraints excluded: chain D residue 14 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.0060 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 191 ASN C 330 GLN D 424 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106277 restraints weight = 12189.450| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.03 r_work: 0.3249 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9175 Z= 0.115 Angle : 0.530 6.690 12480 Z= 0.263 Chirality : 0.039 0.159 1449 Planarity : 0.003 0.033 1589 Dihedral : 7.845 116.418 1321 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.05 % Allowed : 14.46 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.04 (0.24), residues: 1150 helix: -0.52 (0.20), residues: 681 sheet: -2.08 (0.63), residues: 49 loop : -2.57 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 193 TYR 0.009 0.001 TYR C 98 PHE 0.025 0.001 PHE C 569 TRP 0.009 0.001 TRP D 427 HIS 0.004 0.001 HIS C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.11 ( 9175) covalent geometry : angle 0.53007 / 0.26 (12480) hydrogen bonds : bond 0.04190 / 2.77 ( 378) hydrogen bonds : angle 4.12731 / 2.98 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.307 Fit side-chains REVERT: C 67 ARG cc_start: 0.7314 (mtp85) cc_final: 0.6153 (tmm160) REVERT: C 81 ARG cc_start: 0.8321 (mmp80) cc_final: 0.8099 (mtp85) REVERT: C 183 ARG cc_start: 0.8022 (ptm-80) cc_final: 0.7239 (ptp90) REVERT: C 235 GLU cc_start: 0.8137 (tp30) cc_final: 0.7919 (tp30) REVERT: C 520 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7374 (mpp) REVERT: D 306 ASP cc_start: 0.8207 (m-30) cc_final: 0.7947 (m-30) outliers start: 19 outliers final: 4 residues processed: 86 average time/residue: 0.6859 time to fit residues: 62.1532 Evaluate side-chains 75 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 334 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 94 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.0040 chunk 93 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104788 restraints weight = 12171.084| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.10 r_work: 0.3221 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9175 Z= 0.092 Angle : 0.488 6.651 12480 Z= 0.244 Chirality : 0.038 0.147 1449 Planarity : 0.003 0.037 1589 Dihedral : 7.443 110.439 1321 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.94 % Allowed : 15.64 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.25), residues: 1150 helix: -0.18 (0.21), residues: 675 sheet: -1.90 (0.64), residues: 49 loop : -2.42 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 566 TYR 0.007 0.001 TYR C 98 PHE 0.023 0.001 PHE C 569 TRP 0.009 0.001 TRP D 163 HIS 0.003 0.001 HIS C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 ( 9175) covalent geometry : angle 0.48821 / 0.24 (12480) hydrogen bonds : bond 0.03425 / 2.25 ( 378) hydrogen bonds : angle 3.94680 / 2.86 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.220 Fit side-chains REVERT: C 60 MET cc_start: 0.7612 (mmm) cc_final: 0.7276 (mpp) REVERT: C 67 ARG cc_start: 0.7215 (mtp85) cc_final: 0.5958 (tmm160) REVERT: C 107 SER cc_start: 0.7357 (OUTLIER) cc_final: 0.7129 (t) REVERT: C 183 ARG cc_start: 0.7924 (ptm-80) cc_final: 0.7048 (ptp90) REVERT: C 235 GLU cc_start: 0.8067 (tp30) cc_final: 0.7745 (tp30) REVERT: C 343 ASP cc_start: 0.8094 (t0) cc_final: 0.7838 (t0) REVERT: C 520 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7350 (mpp) REVERT: D 306 ASP cc_start: 0.7994 (m-30) cc_final: 0.7787 (m-30) REVERT: D 337 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7586 (ttt90) REVERT: D 566 ARG cc_start: 0.6885 (mtp-110) cc_final: 0.6422 (mtp85) outliers start: 18 outliers final: 8 residues processed: 87 average time/residue: 0.5466 time to fit residues: 50.4965 Evaluate side-chains 80 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 537 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 32 optimal weight: 0.0170 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 191 ASN C 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102291 restraints weight = 12252.447| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.15 r_work: 0.3164 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9175 Z= 0.117 Angle : 0.522 6.720 12480 Z= 0.258 Chirality : 0.039 0.147 1449 Planarity : 0.003 0.032 1589 Dihedral : 7.340 107.623 1321 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.83 % Allowed : 16.29 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.24), residues: 1150 helix: -0.18 (0.21), residues: 682 sheet: -1.77 (0.67), residues: 49 loop : -2.36 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 81 TYR 0.009 0.001 TYR C 98 PHE 0.024 0.001 PHE C 569 TRP 0.009 0.001 TRP D 427 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9175) covalent geometry : angle 0.52191 / 0.26 (12480) hydrogen bonds : bond 0.04147 / 2.74 ( 378) hydrogen bonds : angle 4.01284 / 2.90 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: C 60 MET cc_start: 0.7619 (mmm) cc_final: 0.7308 (mpp) REVERT: C 67 ARG cc_start: 0.7126 (mtp85) cc_final: 0.5885 (tmm160) REVERT: C 107 SER cc_start: 0.7569 (OUTLIER) cc_final: 0.7351 (t) REVERT: C 183 ARG cc_start: 0.7898 (ptm-80) cc_final: 0.7012 (ptp90) REVERT: C 235 GLU cc_start: 0.8085 (tp30) cc_final: 0.7711 (tp30) REVERT: C 356 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8335 (mp) REVERT: C 372 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8287 (mt) REVERT: C 520 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7256 (mpp) REVERT: D 306 ASP cc_start: 0.7990 (m-30) cc_final: 0.7777 (m-30) REVERT: D 337 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7582 (ttt90) REVERT: D 566 ARG cc_start: 0.6867 (mtp-110) cc_final: 0.6454 (mtp85) outliers start: 17 outliers final: 8 residues processed: 88 average time/residue: 0.6204 time to fit residues: 57.7720 Evaluate side-chains 85 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 563 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.0010 chunk 83 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 104 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099661 restraints weight = 12430.611| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.24 r_work: 0.3096 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9175 Z= 0.121 Angle : 0.525 6.766 12480 Z= 0.260 Chirality : 0.039 0.147 1449 Planarity : 0.003 0.032 1589 Dihedral : 7.244 104.614 1321 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.27 % Allowed : 15.75 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.25), residues: 1150 helix: -0.13 (0.21), residues: 682 sheet: -1.70 (0.68), residues: 49 loop : -2.31 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 566 TYR 0.009 0.001 TYR C 98 PHE 0.024 0.001 PHE C 569 TRP 0.009 0.001 TRP D 427 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 9175) covalent geometry : angle 0.52473 / 0.26 (12480) hydrogen bonds : bond 0.04233 / 2.80 ( 378) hydrogen bonds : angle 4.02515 / 2.91 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7109 (mtp85) cc_final: 0.5823 (tmm160) REVERT: C 107 SER cc_start: 0.7509 (OUTLIER) cc_final: 0.7257 (t) REVERT: C 183 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.6995 (ptp90) REVERT: C 235 GLU cc_start: 0.8063 (tp30) cc_final: 0.7650 (tp30) REVERT: C 356 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8297 (mp) REVERT: D 306 ASP cc_start: 0.7914 (m-30) cc_final: 0.7710 (m-30) REVERT: D 337 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7644 (ttt90) REVERT: D 546 ASP cc_start: 0.7819 (t0) cc_final: 0.7427 (t0) REVERT: D 566 ARG cc_start: 0.6845 (mtp-110) cc_final: 0.6477 (mtp85) outliers start: 21 outliers final: 11 residues processed: 90 average time/residue: 0.5866 time to fit residues: 55.7629 Evaluate side-chains 87 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 563 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 114 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 330 GLN C 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104689 restraints weight = 12144.154| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.14 r_work: 0.3199 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9175 Z= 0.090 Angle : 0.485 6.698 12480 Z= 0.241 Chirality : 0.038 0.146 1449 Planarity : 0.003 0.033 1589 Dihedral : 7.029 100.783 1321 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 16.50 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.25), residues: 1150 helix: 0.14 (0.21), residues: 681 sheet: -1.53 (0.68), residues: 49 loop : -2.23 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 193 TYR 0.007 0.001 TYR C 98 PHE 0.022 0.001 PHE C 569 TRP 0.010 0.001 TRP D 163 HIS 0.003 0.001 HIS C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 9175) covalent geometry : angle 0.48529 / 0.24 (12480) hydrogen bonds : bond 0.03342 / 2.21 ( 378) hydrogen bonds : angle 3.84157 / 2.77 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: C 60 MET cc_start: 0.7615 (mmm) cc_final: 0.7319 (mpp) REVERT: C 67 ARG cc_start: 0.7097 (mtp85) cc_final: 0.5872 (tmm160) REVERT: C 107 SER cc_start: 0.7396 (OUTLIER) cc_final: 0.7095 (t) REVERT: C 183 ARG cc_start: 0.7853 (ptm-80) cc_final: 0.6946 (ptp90) REVERT: C 235 GLU cc_start: 0.8084 (tp30) cc_final: 0.7746 (tp30) REVERT: D 337 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7578 (ttt90) REVERT: D 423 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8324 (mmtt) REVERT: D 546 ASP cc_start: 0.7829 (t0) cc_final: 0.7466 (t0) REVERT: D 566 ARG cc_start: 0.6850 (mtp-110) cc_final: 0.6509 (mtp85) outliers start: 17 outliers final: 10 residues processed: 90 average time/residue: 0.5612 time to fit residues: 53.6518 Evaluate side-chains 83 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 563 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100957 restraints weight = 12277.323| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.23 r_work: 0.3115 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9175 Z= 0.108 Angle : 0.516 8.273 12480 Z= 0.254 Chirality : 0.038 0.146 1449 Planarity : 0.003 0.062 1589 Dihedral : 6.990 99.791 1321 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.51 % Allowed : 17.69 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.25), residues: 1150 helix: 0.18 (0.21), residues: 681 sheet: -1.47 (0.68), residues: 49 loop : -2.23 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 193 TYR 0.008 0.001 TYR C 98 PHE 0.022 0.001 PHE C 569 TRP 0.009 0.001 TRP C 16 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 9175) covalent geometry : angle 0.51638 / 0.25 (12480) hydrogen bonds : bond 0.03853 / 2.55 ( 378) hydrogen bonds : angle 3.90618 / 2.82 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: C 60 MET cc_start: 0.7570 (mmm) cc_final: 0.7368 (tpp) REVERT: C 67 ARG cc_start: 0.7064 (mtp85) cc_final: 0.5822 (tmm160) REVERT: C 107 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.7144 (t) REVERT: C 183 ARG cc_start: 0.7828 (ptm-80) cc_final: 0.6920 (ptp90) REVERT: C 235 GLU cc_start: 0.8084 (tp30) cc_final: 0.7678 (tp30) REVERT: C 570 LYS cc_start: 0.8178 (tppt) cc_final: 0.7794 (tptm) REVERT: D 337 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7602 (ttt90) REVERT: D 423 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8296 (mmtt) REVERT: D 546 ASP cc_start: 0.7852 (t0) cc_final: 0.7475 (t0) REVERT: D 566 ARG cc_start: 0.6788 (mtp-110) cc_final: 0.6498 (mtp85) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.7134 time to fit residues: 64.9013 Evaluate side-chains 85 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 563 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 191 ASN C 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102321 restraints weight = 12143.281| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.15 r_work: 0.3168 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9175 Z= 0.119 Angle : 0.527 7.944 12480 Z= 0.259 Chirality : 0.039 0.147 1449 Planarity : 0.004 0.068 1589 Dihedral : 7.052 99.180 1321 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.83 % Allowed : 17.48 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.25), residues: 1150 helix: 0.14 (0.21), residues: 684 sheet: -1.41 (0.68), residues: 50 loop : -2.23 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 193 TYR 0.009 0.001 TYR C 98 PHE 0.023 0.001 PHE C 569 TRP 0.009 0.001 TRP D 427 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 9175) covalent geometry : angle 0.52739 / 0.26 (12480) hydrogen bonds : bond 0.04167 / 2.76 ( 378) hydrogen bonds : angle 3.95930 / 2.86 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7092 (mtp85) cc_final: 0.5896 (tmm160) REVERT: C 107 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.7155 (t) REVERT: C 183 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.6975 (ptp90) REVERT: C 235 GLU cc_start: 0.8076 (tp30) cc_final: 0.7724 (tp30) REVERT: C 396 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: C 570 LYS cc_start: 0.8268 (tppt) cc_final: 0.7904 (tptm) REVERT: D 337 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7602 (ttt90) REVERT: D 423 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8329 (mmtt) REVERT: D 546 ASP cc_start: 0.7855 (t0) cc_final: 0.7561 (t0) REVERT: D 566 ARG cc_start: 0.6879 (mtp-110) cc_final: 0.6599 (mtp85) outliers start: 17 outliers final: 13 residues processed: 86 average time/residue: 0.7188 time to fit residues: 65.2987 Evaluate side-chains 89 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 563 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.098084 restraints weight = 12242.327| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.24 r_work: 0.3076 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9175 Z= 0.150 Angle : 0.569 7.564 12480 Z= 0.279 Chirality : 0.041 0.148 1449 Planarity : 0.004 0.070 1589 Dihedral : 7.251 100.908 1321 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.83 % Allowed : 18.02 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.24), residues: 1150 helix: -0.00 (0.20), residues: 685 sheet: -1.41 (0.69), residues: 49 loop : -2.26 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 193 TYR 0.009 0.001 TYR C 222 PHE 0.024 0.002 PHE C 569 TRP 0.009 0.001 TRP D 427 HIS 0.005 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 9175) covalent geometry : angle 0.56874 / 0.28 (12480) hydrogen bonds : bond 0.04870 / 3.23 ( 378) hydrogen bonds : angle 4.11365 / 2.97 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.27 seconds wall clock time: 43 minutes 26.08 seconds (2606.08 seconds total)