Starting phenix.real_space_refine on Thu Sep 18 09:04:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsi_63356/09_2025/9lsi_63356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsi_63356/09_2025/9lsi_63356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lsi_63356/09_2025/9lsi_63356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsi_63356/09_2025/9lsi_63356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lsi_63356/09_2025/9lsi_63356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsi_63356/09_2025/9lsi_63356.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 9971 2.51 5 N 2519 2.21 5 O 2869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15433 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3182 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 12, 'TRANS': 412} Chain breaks: 1 Chain: "B" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3206 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 418} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1718 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1774 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 5326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5326 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 638} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'CIT': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.12, per 1000 atoms: 0.27 Number of scatterers: 15433 At special positions: 0 Unit cell: (95.7, 121, 196.9, 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 74 16.00 O 2869 8.00 N 2519 7.00 C 9971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS D 358 " distance=2.03 Simple disulfide: pdb=" SG CYS D 295 " - pdb=" SG CYS D 369 " distance=2.03 Simple disulfide: pdb=" SG CYS D 422 " - pdb=" SG CYS D 488 " distance=2.04 Simple disulfide: pdb=" SG CYS E 95 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 649 " - pdb=" SG CYS E 677 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG E1001 " - " ASN E 52 " " NAG E1002 " - " ASN E 124 " " NAG E1003 " - " ASN E 265 " " NAG E1004 " - " ASN E 275 " " NAG E1005 " - " ASN E 398 " " NAG F 1 " - " ASN E 252 " " NAG G 1 " - " ASN E 291 " " NAG I 1 " - " ASN E 413 " " NAG J 1 " - " ASN E 507 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 783.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3628 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 23 sheets defined 40.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.862A pdb=" N PHE A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 54 through 69 removed outlier: 3.639A pdb=" N ILE A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 97 removed outlier: 3.674A pdb=" N VAL A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 112 removed outlier: 3.605A pdb=" N ILE A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.703A pdb=" N LEU A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.892A pdb=" N SER A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 167 removed outlier: 3.924A pdb=" N ILE A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 205 through 237 removed outlier: 3.563A pdb=" N TYR A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 289 removed outlier: 3.750A pdb=" N GLY A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.665A pdb=" N LEU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.611A pdb=" N LYS A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.911A pdb=" N LEU A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.833A pdb=" N ILE A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 384 removed outlier: 3.963A pdb=" N VAL A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.852A pdb=" N THR A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.503A pdb=" N ALA A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 414 Processing helix chain 'A' and resid 419 through 446 removed outlier: 3.520A pdb=" N GLN A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.540A pdb=" N THR B 37 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 71 removed outlier: 3.849A pdb=" N ALA B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.509A pdb=" N TYR B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 removed outlier: 3.575A pdb=" N ILE B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 removed outlier: 4.109A pdb=" N VAL B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.844A pdb=" N LEU B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 144 removed outlier: 4.586A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 167 removed outlier: 3.544A pdb=" N PHE B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.750A pdb=" N MET B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.846A pdb=" N ILE B 181 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 182' Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.558A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 237 removed outlier: 4.131A pdb=" N ALA B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 288 removed outlier: 3.951A pdb=" N THR B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.793A pdb=" N TRP B 303 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.586A pdb=" N LYS B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 removed outlier: 4.075A pdb=" N VAL B 342 " --> pdb=" O TRP B 338 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.764A pdb=" N ILE B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 383 removed outlier: 3.578A pdb=" N VAL B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.702A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 389 through 394' Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 406 through 414 removed outlier: 3.682A pdb=" N SER B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 446 removed outlier: 4.401A pdb=" N GLY B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 56 removed outlier: 3.764A pdb=" N SER C 56 " --> pdb=" O TYR C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'E' and resid 67 through 75 removed outlier: 4.222A pdb=" N TYR E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 98 Processing helix chain 'E' and resid 117 through 121 removed outlier: 4.395A pdb=" N PHE E 121 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.664A pdb=" N LEU E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 196 removed outlier: 4.353A pdb=" N ASN E 196 " --> pdb=" O ILE E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 193 through 196' Processing helix chain 'E' and resid 215 through 221 removed outlier: 3.650A pdb=" N GLY E 221 " --> pdb=" O PHE E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 removed outlier: 3.899A pdb=" N LEU E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 274 removed outlier: 3.674A pdb=" N PHE E 268 " --> pdb=" O ASN E 265 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 269 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY E 270 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP E 273 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 449 through 453 removed outlier: 3.858A pdb=" N TRP E 452 " --> pdb=" O GLY E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 526 removed outlier: 4.024A pdb=" N LEU E 526 " --> pdb=" O ASP E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 547 removed outlier: 4.205A pdb=" N TRP E 546 " --> pdb=" O LEU E 542 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS E 547 " --> pdb=" O ALA E 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 542 through 547' Processing helix chain 'E' and resid 650 through 663 removed outlier: 3.754A pdb=" N ALA E 655 " --> pdb=" O CYS E 651 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TRP E 656 " --> pdb=" O GLU E 652 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE E 657 " --> pdb=" O SER E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 675 removed outlier: 3.606A pdb=" N HIS E 674 " --> pdb=" O GLU E 670 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR E 675 " --> pdb=" O LEU E 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 670 through 675' Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.995A pdb=" N GLY C 16 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 18 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN C 84 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU C 20 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN C 82 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N CYS C 22 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 80 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA C 24 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR C 78 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.282A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 33 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL C 108 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.282A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 33 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.879A pdb=" N ASP C 194 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 187 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 134 through 136 removed outlier: 6.965A pdb=" N LEU C 135 " --> pdb=" O ILE C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 157 through 162 Processing sheet with id=AA9, first strand: chain 'D' and resid 276 through 279 removed outlier: 3.547A pdb=" N LEU D 291 " --> pdb=" O MET D 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 283 through 284 removed outlier: 3.558A pdb=" N VAL D 390 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 372 " --> pdb=" O TRP D 306 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TRP D 306 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY D 322 " --> pdb=" O TRP D 309 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG D 311 " --> pdb=" O TRP D 320 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP D 320 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR D 330 " --> pdb=" O ASP D 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 403 through 405 removed outlier: 3.634A pdb=" N LEU D 473 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 472 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER D 465 " --> pdb=" O THR D 472 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 410 through 412 removed outlier: 3.603A pdb=" N GLU D 505 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 485 " --> pdb=" O GLN D 438 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP D 435 " --> pdb=" O LEU D 447 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 410 through 412 removed outlier: 3.603A pdb=" N GLU D 505 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 485 " --> pdb=" O GLN D 438 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN D 490 " --> pdb=" O THR D 497 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.602A pdb=" N ALA E 35 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY E 83 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 80 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN E 105 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL E 82 " --> pdb=" O ASN E 105 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN E 107 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU E 104 " --> pdb=" O HIS E 129 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET E 131 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU E 106 " --> pdb=" O MET E 131 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 177 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU E 176 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS E 200 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER E 256 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AB7, first strand: chain 'E' and resid 262 through 263 removed outlier: 3.623A pdb=" N THR E 263 " --> pdb=" O VAL E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 302 through 304 Processing sheet with id=AB9, first strand: chain 'E' and resid 312 through 313 Processing sheet with id=AC1, first strand: chain 'E' and resid 360 through 361 removed outlier: 3.636A pdb=" N SER E 385 " --> pdb=" O LEU E 360 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 437 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU E 436 " --> pdb=" O TYR E 462 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE E 461 " --> pdb=" O MET E 486 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU E 485 " --> pdb=" O ASP E 512 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 395 through 396 Processing sheet with id=AC3, first strand: chain 'E' and resid 444 through 446 removed outlier: 7.139A pdb=" N GLN E 445 " --> pdb=" O GLN E 470 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU E 469 " --> pdb=" O LYS E 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 534 through 536 removed outlier: 3.646A pdb=" N ASN E 568 " --> pdb=" O LEU E 535 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 676 through 677 588 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.91 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: 4644 1.33 - 1.46: 2770 1.46 - 1.58: 8218 1.58 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 15751 Sorted by residual: bond pdb=" N VAL C 143 " pdb=" CA VAL C 143 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.15e-02 7.56e+03 1.10e+01 bond pdb=" N ILE C 230 " pdb=" CA ILE C 230 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.24e-02 6.50e+03 9.65e+00 bond pdb=" N VAL C 139 " pdb=" CA VAL C 139 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.33e+00 bond pdb=" N VAL C 5 " pdb=" CA VAL C 5 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 8.91e+00 bond pdb=" N ASP C 141 " pdb=" CA ASP C 141 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.42e+00 ... (remaining 15746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 20419 1.68 - 3.36: 794 3.36 - 5.04: 134 5.04 - 6.72: 28 6.72 - 8.39: 3 Bond angle restraints: 21378 Sorted by residual: angle pdb=" N THR E 78 " pdb=" CA THR E 78 " pdb=" C THR E 78 " ideal model delta sigma weight residual 113.72 107.31 6.41 1.30e+00 5.92e-01 2.43e+01 angle pdb=" CA GLY D 395 " pdb=" C GLY D 395 " pdb=" O GLY D 395 " ideal model delta sigma weight residual 121.77 118.04 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" CA LYS D 286 " pdb=" C LYS D 286 " pdb=" N PRO D 287 " ideal model delta sigma weight residual 117.51 122.35 -4.84 1.13e+00 7.83e-01 1.83e+01 angle pdb=" N PRO D 287 " pdb=" CA PRO D 287 " pdb=" C PRO D 287 " ideal model delta sigma weight residual 112.47 104.08 8.39 2.06e+00 2.36e-01 1.66e+01 angle pdb=" N SER D 290 " pdb=" CA SER D 290 " pdb=" C SER D 290 " ideal model delta sigma weight residual 108.75 115.56 -6.81 1.71e+00 3.42e-01 1.58e+01 ... (remaining 21373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.46: 8936 22.46 - 44.92: 442 44.92 - 67.38: 44 67.38 - 89.84: 19 89.84 - 112.30: 17 Dihedral angle restraints: 9458 sinusoidal: 3783 harmonic: 5675 Sorted by residual: dihedral pdb=" CB CYS C 85 " pdb=" SG CYS C 85 " pdb=" SG CYS D 358 " pdb=" CB CYS D 358 " ideal model delta sinusoidal sigma weight residual 93.00 155.02 -62.02 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CA SER D 383 " pdb=" C SER D 383 " pdb=" N TRP D 384 " pdb=" CA TRP D 384 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA TYR D 374 " pdb=" C TYR D 374 " pdb=" N GLN D 375 " pdb=" CA GLN D 375 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 9455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 2525 0.243 - 0.485: 6 0.485 - 0.728: 1 0.728 - 0.970: 1 0.970 - 1.213: 2 Chirality restraints: 2535 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.75e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.64e+01 chirality pdb=" C1 NAG I 3 " pdb=" O4 NAG I 2 " pdb=" C2 NAG I 3 " pdb=" O5 NAG I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.40e+01 ... (remaining 2532 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.169 2.00e-02 2.50e+03 1.41e-01 2.49e+02 pdb=" C7 NAG F 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.232 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.048 2.00e-02 2.50e+03 3.94e-02 1.94e+01 pdb=" C7 NAG J 2 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.063 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.045 2.00e-02 2.50e+03 3.68e-02 1.70e+01 pdb=" C7 NAG J 1 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.059 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.008 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2184 2.75 - 3.29: 15129 3.29 - 3.82: 23730 3.82 - 4.36: 27213 4.36 - 4.90: 48052 Nonbonded interactions: 116308 Sorted by model distance: nonbonded pdb=" OD1 ASP E 116 " pdb=" NZ LYS E 139 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASN E 309 " pdb=" OG1 THR E 334 " model vdw 2.235 3.040 nonbonded pdb=" OG SER E 112 " pdb=" O ASN E 133 " model vdw 2.237 3.040 nonbonded pdb=" O CYS E 122 " pdb=" NE2 GLN E 146 " model vdw 2.255 3.120 nonbonded pdb=" O SER E 134 " pdb=" NE2 GLN E 136 " model vdw 2.297 3.120 ... (remaining 116303 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 'A' and (resid 16 through 251 or (resid 258 through 259 and (name N or na \ me CA or name C or name O or name CB )) or resid 260 through 446)) selection = (chain 'B' and (resid 16 through 251 or resid 258 through 446)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.280 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 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 : 0.006 0.054 15770 Z= 0.349 Angle : 0.833 16.220 21430 Z= 0.471 Chirality : 0.065 1.213 2535 Planarity : 0.005 0.141 2664 Dihedral : 14.349 112.300 5815 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 0.54 % Allowed : 0.85 % Favored : 98.61 % 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 aren not related in a simple way. whole: -1.17 (0.19), residues: 1974 helix: 0.53 (0.20), residues: 669 sheet: -0.71 (0.32), residues: 297 loop : -1.74 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 489 TYR 0.027 0.002 TYR C 173 PHE 0.029 0.002 PHE B 55 TRP 0.010 0.001 TRP C 36 HIS 0.003 0.001 HIS E 359 Details of bonding type rmsd covalent geometry : bond 0.00644 (15751) covalent geometry : angle 0.77404 (21378) SS BOND : bond 0.00498 ( 5) SS BOND : angle 3.76141 ( 10) hydrogen bonds : bond 0.23370 ( 571) hydrogen bonds : angle 6.71707 ( 1662) link_BETA1-4 : bond 0.04547 ( 5) link_BETA1-4 : angle 7.69987 ( 15) link_NAG-ASN : bond 0.01528 ( 9) link_NAG-ASN : angle 6.13147 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8351 (t0) cc_final: 0.7636 (t0) REVERT: C 76 LYS cc_start: 0.9310 (mppt) cc_final: 0.8875 (mtmm) REVERT: D 405 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: E 278 MET cc_start: 0.8953 (tmm) cc_final: 0.7927 (tmm) outliers start: 9 outliers final: 2 residues processed: 90 average time/residue: 0.1382 time to fit residues: 18.8272 Evaluate side-chains 65 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 74 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** E 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.052924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033998 restraints weight = 79098.691| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.97 r_work: 0.2514 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15770 Z= 0.193 Angle : 0.655 12.525 21430 Z= 0.335 Chirality : 0.045 0.478 2535 Planarity : 0.003 0.036 2664 Dihedral : 10.795 99.451 2425 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.42 % Allowed : 5.57 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.19), residues: 1974 helix: 0.80 (0.20), residues: 692 sheet: -0.62 (0.32), residues: 292 loop : -1.71 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 331 TYR 0.018 0.001 TYR C 173 PHE 0.016 0.001 PHE B 87 TRP 0.019 0.001 TRP E 656 HIS 0.004 0.001 HIS E 129 Details of bonding type rmsd covalent geometry : bond 0.00441 (15751) covalent geometry : angle 0.62886 (21378) SS BOND : bond 0.00530 ( 5) SS BOND : angle 1.53711 ( 10) hydrogen bonds : bond 0.06635 ( 571) hydrogen bonds : angle 5.00079 ( 1662) link_BETA1-4 : bond 0.00379 ( 5) link_BETA1-4 : angle 2.95087 ( 15) link_NAG-ASN : bond 0.00826 ( 9) link_NAG-ASN : angle 4.65490 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.563 Fit side-chains REVERT: C 73 ASP cc_start: 0.8777 (t0) cc_final: 0.7747 (t0) REVERT: C 76 LYS cc_start: 0.9505 (mppt) cc_final: 0.9131 (mtmm) REVERT: D 412 LEU cc_start: 0.9330 (mt) cc_final: 0.9125 (mp) REVERT: E 278 MET cc_start: 0.9127 (tmm) cc_final: 0.8250 (tmm) outliers start: 7 outliers final: 3 residues processed: 67 average time/residue: 0.1266 time to fit residues: 13.7188 Evaluate side-chains 63 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain E residue 74 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 53 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 220 ASN C 224 GLN ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS E 572 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.051767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.032688 restraints weight = 80192.499| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 3.97 r_work: 0.2502 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15770 Z= 0.287 Angle : 0.699 12.836 21430 Z= 0.354 Chirality : 0.046 0.458 2535 Planarity : 0.003 0.034 2664 Dihedral : 9.888 98.159 2418 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.85 % Allowed : 9.44 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.19), residues: 1974 helix: 0.88 (0.20), residues: 694 sheet: -0.87 (0.31), residues: 293 loop : -1.75 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 65 TYR 0.022 0.002 TYR C 173 PHE 0.019 0.001 PHE C 68 TRP 0.018 0.001 TRP E 656 HIS 0.004 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00665 (15751) covalent geometry : angle 0.67825 (21378) SS BOND : bond 0.00518 ( 5) SS BOND : angle 1.12638 ( 10) hydrogen bonds : bond 0.06957 ( 571) hydrogen bonds : angle 4.91114 ( 1662) link_BETA1-4 : bond 0.00528 ( 5) link_BETA1-4 : angle 2.92340 ( 15) link_NAG-ASN : bond 0.00751 ( 9) link_NAG-ASN : angle 4.31987 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 444 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8286 (ttt) REVERT: C 73 ASP cc_start: 0.8818 (t0) cc_final: 0.8180 (t0) REVERT: D 366 MET cc_start: 0.9061 (mmm) cc_final: 0.8812 (tpt) REVERT: E 278 MET cc_start: 0.9150 (tmm) cc_final: 0.8108 (tmm) outliers start: 14 outliers final: 7 residues processed: 70 average time/residue: 0.1081 time to fit residues: 12.6157 Evaluate side-chains 67 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 41 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 GLN ** 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 = 0.3268 r_free = 0.3268 target = 0.052363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.033213 restraints weight = 79539.925| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 4.12 r_work: 0.2479 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15770 Z= 0.193 Angle : 0.598 11.860 21430 Z= 0.305 Chirality : 0.044 0.440 2535 Planarity : 0.003 0.035 2664 Dihedral : 9.142 95.514 2418 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.15 % Allowed : 10.47 % Favored : 88.38 % 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 aren not related in a simple way. whole: -0.77 (0.19), residues: 1974 helix: 1.15 (0.20), residues: 695 sheet: -0.73 (0.31), residues: 298 loop : -1.71 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 417 TYR 0.016 0.001 TYR C 173 PHE 0.014 0.001 PHE C 68 TRP 0.014 0.001 TRP E 656 HIS 0.007 0.001 HIS E 682 Details of bonding type rmsd covalent geometry : bond 0.00445 (15751) covalent geometry : angle 0.57568 (21378) SS BOND : bond 0.00401 ( 5) SS BOND : angle 0.63312 ( 10) hydrogen bonds : bond 0.05771 ( 571) hydrogen bonds : angle 4.58144 ( 1662) link_BETA1-4 : bond 0.00430 ( 5) link_BETA1-4 : angle 3.00617 ( 15) link_NAG-ASN : bond 0.00765 ( 9) link_NAG-ASN : angle 4.05665 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.618 Fit side-chains REVERT: B 389 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9257 (mt) REVERT: C 76 LYS cc_start: 0.9571 (mppt) cc_final: 0.9284 (mtmm) REVERT: D 366 MET cc_start: 0.8931 (mmm) cc_final: 0.8071 (mmm) REVERT: E 278 MET cc_start: 0.9105 (tmm) cc_final: 0.8137 (tmm) outliers start: 19 outliers final: 11 residues processed: 76 average time/residue: 0.1108 time to fit residues: 13.8985 Evaluate side-chains 71 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 133 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 65 optimal weight: 0.0670 chunk 145 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN ** E 146 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 = 0.3287 r_free = 0.3287 target = 0.052833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.033881 restraints weight = 79508.142| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.10 r_work: 0.2497 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15770 Z= 0.144 Angle : 0.562 11.374 21430 Z= 0.284 Chirality : 0.043 0.432 2535 Planarity : 0.003 0.033 2664 Dihedral : 8.734 93.691 2418 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.33 % Allowed : 10.34 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.19), residues: 1974 helix: 1.40 (0.21), residues: 693 sheet: -0.71 (0.31), residues: 293 loop : -1.67 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 417 TYR 0.019 0.001 TYR C 173 PHE 0.012 0.001 PHE A 33 TRP 0.012 0.001 TRP C 159 HIS 0.003 0.001 HIS E 359 Details of bonding type rmsd covalent geometry : bond 0.00326 (15751) covalent geometry : angle 0.53890 (21378) SS BOND : bond 0.00489 ( 5) SS BOND : angle 1.02707 ( 10) hydrogen bonds : bond 0.05287 ( 571) hydrogen bonds : angle 4.38023 ( 1662) link_BETA1-4 : bond 0.00494 ( 5) link_BETA1-4 : angle 2.96991 ( 15) link_NAG-ASN : bond 0.00762 ( 9) link_NAG-ASN : angle 3.90339 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.631 Fit side-chains REVERT: A 290 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9054 (tt) REVERT: B 389 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9230 (mt) REVERT: C 34 MET cc_start: 0.9391 (mmm) cc_final: 0.9187 (mmm) REVERT: C 76 LYS cc_start: 0.9577 (mppt) cc_final: 0.9267 (mtmm) REVERT: D 364 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8196 (t) REVERT: D 381 PHE cc_start: 0.4122 (OUTLIER) cc_final: 0.2872 (t80) REVERT: E 278 MET cc_start: 0.9129 (tmm) cc_final: 0.8148 (tmm) outliers start: 22 outliers final: 10 residues processed: 79 average time/residue: 0.1145 time to fit residues: 14.8121 Evaluate side-chains 72 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 155 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 17 optimal weight: 0.0000 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN ** E 146 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 = 0.3286 r_free = 0.3286 target = 0.052946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.033857 restraints weight = 79080.104| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 4.11 r_work: 0.2502 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15770 Z= 0.143 Angle : 0.556 11.089 21430 Z= 0.280 Chirality : 0.042 0.422 2535 Planarity : 0.003 0.033 2664 Dihedral : 8.322 91.783 2418 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.45 % Allowed : 10.89 % Favored : 87.66 % 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 aren not related in a simple way. whole: -0.50 (0.19), residues: 1974 helix: 1.51 (0.21), residues: 695 sheet: -0.66 (0.31), residues: 293 loop : -1.64 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 65 TYR 0.017 0.001 TYR C 173 PHE 0.012 0.001 PHE B 87 TRP 0.012 0.001 TRP E 656 HIS 0.003 0.001 HIS E 359 Details of bonding type rmsd covalent geometry : bond 0.00325 (15751) covalent geometry : angle 0.53429 (21378) SS BOND : bond 0.00332 ( 5) SS BOND : angle 0.79328 ( 10) hydrogen bonds : bond 0.05036 ( 571) hydrogen bonds : angle 4.25616 ( 1662) link_BETA1-4 : bond 0.00532 ( 5) link_BETA1-4 : angle 2.93651 ( 15) link_NAG-ASN : bond 0.00725 ( 9) link_NAG-ASN : angle 3.75884 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: B 389 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9227 (mt) REVERT: C 76 LYS cc_start: 0.9590 (mppt) cc_final: 0.9265 (mtmm) REVERT: D 364 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8168 (t) REVERT: D 366 MET cc_start: 0.8901 (mmm) cc_final: 0.8218 (mmm) REVERT: D 381 PHE cc_start: 0.4151 (OUTLIER) cc_final: 0.2858 (t80) REVERT: E 278 MET cc_start: 0.9140 (tmm) cc_final: 0.8257 (tmm) REVERT: E 486 MET cc_start: 0.9343 (mmm) cc_final: 0.9057 (mmm) outliers start: 24 outliers final: 14 residues processed: 81 average time/residue: 0.1184 time to fit residues: 15.8128 Evaluate side-chains 76 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN ** E 146 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 = 0.3273 r_free = 0.3273 target = 0.052321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.033311 restraints weight = 78943.770| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 4.07 r_work: 0.2517 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15770 Z= 0.193 Angle : 0.597 11.348 21430 Z= 0.300 Chirality : 0.043 0.419 2535 Planarity : 0.003 0.034 2664 Dihedral : 8.057 90.402 2418 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.39 % Allowed : 11.43 % Favored : 87.17 % 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 aren not related in a simple way. whole: -0.50 (0.19), residues: 1974 helix: 1.51 (0.21), residues: 696 sheet: -0.64 (0.31), residues: 307 loop : -1.67 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 489 TYR 0.021 0.001 TYR C 173 PHE 0.015 0.001 PHE B 87 TRP 0.014 0.001 TRP E 656 HIS 0.003 0.001 HIS D 489 Details of bonding type rmsd covalent geometry : bond 0.00445 (15751) covalent geometry : angle 0.57809 (21378) SS BOND : bond 0.00369 ( 5) SS BOND : angle 0.71488 ( 10) hydrogen bonds : bond 0.05548 ( 571) hydrogen bonds : angle 4.34267 ( 1662) link_BETA1-4 : bond 0.00509 ( 5) link_BETA1-4 : angle 2.87372 ( 15) link_NAG-ASN : bond 0.00664 ( 9) link_NAG-ASN : angle 3.69634 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.645 Fit side-chains REVERT: A 290 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9090 (tt) REVERT: B 389 ILE cc_start: 0.9534 (OUTLIER) cc_final: 0.9224 (mt) REVERT: C 76 LYS cc_start: 0.9570 (mppt) cc_final: 0.9215 (mtmm) REVERT: D 364 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8258 (t) REVERT: D 366 MET cc_start: 0.8963 (mmm) cc_final: 0.8331 (mmm) REVERT: D 381 PHE cc_start: 0.4262 (OUTLIER) cc_final: 0.2942 (t80) REVERT: E 278 MET cc_start: 0.9184 (tmm) cc_final: 0.8189 (tmm) REVERT: E 374 MET cc_start: 0.9287 (ttm) cc_final: 0.8987 (mtm) outliers start: 23 outliers final: 14 residues processed: 78 average time/residue: 0.1166 time to fit residues: 14.9760 Evaluate side-chains 75 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 88 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 64 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN C 224 GLN ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.034320 restraints weight = 79253.132| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 4.12 r_work: 0.2512 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15770 Z= 0.126 Angle : 0.547 10.746 21430 Z= 0.274 Chirality : 0.042 0.410 2535 Planarity : 0.003 0.033 2664 Dihedral : 7.619 88.326 2418 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.15 % Allowed : 11.80 % Favored : 87.05 % 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 aren not related in a simple way. whole: -0.38 (0.20), residues: 1974 helix: 1.63 (0.21), residues: 697 sheet: -0.63 (0.31), residues: 293 loop : -1.58 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.015 0.001 TYR B 31 PHE 0.012 0.001 PHE A 33 TRP 0.011 0.001 TRP E 656 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00284 (15751) covalent geometry : angle 0.52674 (21378) SS BOND : bond 0.00304 ( 5) SS BOND : angle 1.45355 ( 10) hydrogen bonds : bond 0.04745 ( 571) hydrogen bonds : angle 4.13114 ( 1662) link_BETA1-4 : bond 0.00553 ( 5) link_BETA1-4 : angle 2.87006 ( 15) link_NAG-ASN : bond 0.00724 ( 9) link_NAG-ASN : angle 3.56033 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.653 Fit side-chains REVERT: A 290 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8999 (tt) REVERT: B 389 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9168 (mt) REVERT: C 76 LYS cc_start: 0.9586 (mppt) cc_final: 0.9196 (mtmm) REVERT: D 364 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8136 (t) REVERT: D 366 MET cc_start: 0.8913 (mmm) cc_final: 0.8154 (mmm) REVERT: D 381 PHE cc_start: 0.4379 (OUTLIER) cc_final: 0.3093 (t80) REVERT: D 412 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9322 (mm) REVERT: E 278 MET cc_start: 0.9166 (tmm) cc_final: 0.8238 (tmm) REVERT: E 374 MET cc_start: 0.9346 (ttm) cc_final: 0.8945 (mtm) REVERT: E 486 MET cc_start: 0.9261 (mmm) cc_final: 0.9032 (mmm) outliers start: 19 outliers final: 10 residues processed: 76 average time/residue: 0.1198 time to fit residues: 15.0134 Evaluate side-chains 73 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 122 optimal weight: 0.0980 chunk 185 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 138 optimal weight: 0.0870 chunk 121 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN ** E 146 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 = 0.3328 r_free = 0.3328 target = 0.054572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.035661 restraints weight = 77954.657| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 4.17 r_work: 0.2566 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 15770 Z= 0.091 Angle : 0.523 10.122 21430 Z= 0.259 Chirality : 0.041 0.395 2535 Planarity : 0.003 0.033 2664 Dihedral : 7.018 85.702 2418 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.09 % Allowed : 11.98 % Favored : 86.93 % 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 aren not related in a simple way. whole: -0.25 (0.20), residues: 1974 helix: 1.81 (0.21), residues: 687 sheet: -0.37 (0.33), residues: 276 loop : -1.58 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 416 TYR 0.015 0.001 TYR B 31 PHE 0.011 0.001 PHE A 33 TRP 0.011 0.001 TRP B 382 HIS 0.004 0.000 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00189 (15751) covalent geometry : angle 0.50290 (21378) SS BOND : bond 0.00270 ( 5) SS BOND : angle 1.34687 ( 10) hydrogen bonds : bond 0.03723 ( 571) hydrogen bonds : angle 3.88838 ( 1662) link_BETA1-4 : bond 0.00691 ( 5) link_BETA1-4 : angle 2.89387 ( 15) link_NAG-ASN : bond 0.00778 ( 9) link_NAG-ASN : angle 3.42889 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.638 Fit side-chains REVERT: A 290 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 389 ILE cc_start: 0.9624 (OUTLIER) cc_final: 0.9319 (mt) REVERT: C 76 LYS cc_start: 0.9597 (mppt) cc_final: 0.9262 (mtmm) REVERT: D 364 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8072 (t) REVERT: D 366 MET cc_start: 0.8874 (mmm) cc_final: 0.8148 (mmm) REVERT: D 381 PHE cc_start: 0.4225 (OUTLIER) cc_final: 0.2932 (t80) REVERT: E 278 MET cc_start: 0.9171 (tmm) cc_final: 0.8315 (tmm) REVERT: E 374 MET cc_start: 0.9272 (ttm) cc_final: 0.8973 (mtm) REVERT: E 486 MET cc_start: 0.9251 (mmm) cc_final: 0.9008 (mmm) outliers start: 18 outliers final: 8 residues processed: 81 average time/residue: 0.1160 time to fit residues: 15.3197 Evaluate side-chains 74 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 9 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 165 optimal weight: 0.3980 chunk 136 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN ** E 146 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 = 0.3330 r_free = 0.3330 target = 0.054637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035676 restraints weight = 78273.763| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 4.17 r_work: 0.2569 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 15770 Z= 0.094 Angle : 0.539 12.890 21430 Z= 0.265 Chirality : 0.041 0.390 2535 Planarity : 0.003 0.033 2664 Dihedral : 6.739 84.303 2418 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.85 % Allowed : 12.16 % Favored : 86.99 % 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 aren not related in a simple way. whole: -0.17 (0.20), residues: 1974 helix: 1.90 (0.21), residues: 684 sheet: -0.27 (0.33), residues: 276 loop : -1.56 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.014 0.001 TYR B 31 PHE 0.011 0.001 PHE A 33 TRP 0.011 0.001 TRP B 382 HIS 0.004 0.000 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00205 (15751) covalent geometry : angle 0.51966 (21378) SS BOND : bond 0.00243 ( 5) SS BOND : angle 1.15943 ( 10) hydrogen bonds : bond 0.03721 ( 571) hydrogen bonds : angle 3.84239 ( 1662) link_BETA1-4 : bond 0.00617 ( 5) link_BETA1-4 : angle 2.85991 ( 15) link_NAG-ASN : bond 0.00727 ( 9) link_NAG-ASN : angle 3.39242 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.654 Fit side-chains REVERT: A 290 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8829 (tt) REVERT: B 389 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9331 (mt) REVERT: C 76 LYS cc_start: 0.9574 (mppt) cc_final: 0.9183 (mtmm) REVERT: D 364 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8147 (t) REVERT: D 366 MET cc_start: 0.8816 (mmm) cc_final: 0.8103 (mmm) REVERT: D 381 PHE cc_start: 0.4119 (OUTLIER) cc_final: 0.3035 (t80) REVERT: D 412 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9264 (mm) REVERT: E 278 MET cc_start: 0.9165 (tmm) cc_final: 0.8306 (tmm) REVERT: E 374 MET cc_start: 0.9300 (ttm) cc_final: 0.8947 (mtm) REVERT: E 486 MET cc_start: 0.9264 (mmm) cc_final: 0.9024 (mmm) outliers start: 14 outliers final: 7 residues processed: 77 average time/residue: 0.1200 time to fit residues: 14.9106 Evaluate side-chains 75 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 43 optimal weight: 0.0980 chunk 143 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 146 optimal weight: 30.0000 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 GLN ** 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 = 0.3332 r_free = 0.3332 target = 0.054719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.035779 restraints weight = 77737.299| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 4.15 r_work: 0.2571 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15770 Z= 0.096 Angle : 0.534 11.799 21430 Z= 0.262 Chirality : 0.041 0.387 2535 Planarity : 0.003 0.032 2664 Dihedral : 6.435 82.391 2418 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.79 % Allowed : 12.16 % Favored : 87.05 % 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 aren not related in a simple way. whole: -0.11 (0.20), residues: 1974 helix: 1.91 (0.21), residues: 686 sheet: -0.21 (0.34), residues: 276 loop : -1.52 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.015 0.001 TYR B 31 PHE 0.011 0.001 PHE A 33 TRP 0.013 0.001 TRP D 320 HIS 0.003 0.000 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00212 (15751) covalent geometry : angle 0.51550 (21378) SS BOND : bond 0.00262 ( 5) SS BOND : angle 1.09926 ( 10) hydrogen bonds : bond 0.03721 ( 571) hydrogen bonds : angle 3.80833 ( 1662) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 2.80390 ( 15) link_NAG-ASN : bond 0.00703 ( 9) link_NAG-ASN : angle 3.31047 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4032.57 seconds wall clock time: 69 minutes 51.42 seconds (4191.42 seconds total)