Starting phenix.real_space_refine on Sat May 17 10:15:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsi_63356/05_2025/9lsi_63356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsi_63356/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lsi_63356/05_2025/9lsi_63356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsi_63356/05_2025/9lsi_63356.map" model { file = "/net/cci-nas-00/data/ceres_data/9lsi_63356/05_2025/9lsi_63356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsi_63356/05_2025/9lsi_63356.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: 8.60, per 1000 atoms: 0.56 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: 4.01 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.14 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: 4.76 Time building geometry restraints manager: 4.53 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: 1.200 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.560 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- 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 : 8.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (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 TRP 0.010 0.001 TRP C 36 HIS 0.003 0.001 HIS E 359 PHE 0.029 0.002 PHE B 55 TYR 0.027 0.002 TYR C 173 ARG 0.004 0.001 ARG E 489 Details of bonding type rmsd link_NAG-ASN : bond 0.01528 ( 9) link_NAG-ASN : angle 6.13147 ( 27) link_BETA1-4 : bond 0.04547 ( 5) link_BETA1-4 : angle 7.69987 ( 15) hydrogen bonds : bond 0.23370 ( 571) hydrogen bonds : angle 6.71707 ( 1662) SS BOND : bond 0.00498 ( 5) SS BOND : angle 3.76141 ( 10) covalent geometry : bond 0.00644 (15751) covalent geometry : angle 0.77404 (21378) *********************** 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 : 1.776 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: 0.2901 time to fit residues: 39.6066 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 : 1.805 ------------------------------------------------------------------------------- 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 166 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 684 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.052804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.033880 restraints weight = 78949.054| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 3.96 r_work: 0.2510 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15770 Z= 0.204 Angle : 0.660 12.696 21430 Z= 0.338 Chirality : 0.045 0.475 2535 Planarity : 0.003 0.036 2664 Dihedral : 10.826 99.805 2425 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.42 % Allowed : 5.69 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1974 helix: 0.84 (0.21), residues: 686 sheet: -0.66 (0.32), residues: 294 loop : -1.68 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 656 HIS 0.004 0.001 HIS E 129 PHE 0.016 0.001 PHE B 87 TYR 0.019 0.002 TYR C 173 ARG 0.005 0.000 ARG E 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 9) link_NAG-ASN : angle 4.66018 ( 27) link_BETA1-4 : bond 0.00297 ( 5) link_BETA1-4 : angle 2.95515 ( 15) hydrogen bonds : bond 0.06751 ( 571) hydrogen bonds : angle 5.02577 ( 1662) SS BOND : bond 0.00527 ( 5) SS BOND : angle 1.55191 ( 10) covalent geometry : bond 0.00465 (15751) covalent geometry : angle 0.63436 (21378) *********************** 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 : 1.934 Fit side-chains REVERT: C 73 ASP cc_start: 0.8784 (t0) cc_final: 0.7757 (t0) REVERT: C 76 LYS cc_start: 0.9500 (mppt) cc_final: 0.9128 (mtmm) REVERT: D 405 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8837 (mt0) REVERT: D 412 LEU cc_start: 0.9339 (mt) cc_final: 0.9110 (mp) REVERT: E 278 MET cc_start: 0.9117 (tmm) cc_final: 0.8106 (tmm) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.2683 time to fit residues: 28.8570 Evaluate side-chains 65 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 656 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 154 optimal weight: 30.0000 chunk 181 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 0.0060 chunk 7 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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 ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.052858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.033941 restraints weight = 78997.532| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.97 r_work: 0.2515 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15770 Z= 0.177 Angle : 0.602 12.070 21430 Z= 0.306 Chirality : 0.044 0.453 2535 Planarity : 0.003 0.034 2664 Dihedral : 9.866 97.791 2421 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.73 % Allowed : 8.59 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1974 helix: 0.97 (0.20), residues: 695 sheet: -0.67 (0.32), residues: 296 loop : -1.70 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 656 HIS 0.003 0.001 HIS E 359 PHE 0.013 0.001 PHE B 87 TYR 0.019 0.001 TYR C 173 ARG 0.005 0.000 ARG E 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 9) link_NAG-ASN : angle 4.30629 ( 27) link_BETA1-4 : bond 0.00360 ( 5) link_BETA1-4 : angle 2.95565 ( 15) hydrogen bonds : bond 0.06007 ( 571) hydrogen bonds : angle 4.66343 ( 1662) SS BOND : bond 0.00399 ( 5) SS BOND : angle 0.86351 ( 10) covalent geometry : bond 0.00407 (15751) covalent geometry : angle 0.57762 (21378) *********************** 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 75 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.703 Fit side-chains revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8710 (t0) cc_final: 0.8032 (t0) REVERT: D 366 MET cc_start: 0.9007 (mmm) cc_final: 0.8755 (tpt) REVERT: D 405 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8665 (mt0) REVERT: D 412 LEU cc_start: 0.9281 (mt) cc_final: 0.9038 (mp) REVERT: E 162 THR cc_start: 0.9606 (OUTLIER) cc_final: 0.9393 (m) REVERT: E 278 MET cc_start: 0.9144 (tmm) cc_final: 0.8099 (tmm) REVERT: E 374 MET cc_start: 0.9333 (ttm) cc_final: 0.9018 (ttm) outliers start: 12 outliers final: 6 residues processed: 72 average time/residue: 0.2487 time to fit residues: 29.1892 Evaluate side-chains 68 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 74 TYR Chi-restraints excluded: chain E residue 162 THR 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 29 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 132 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** E 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.035376 restraints weight = 77716.716| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 4.14 r_work: 0.2555 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15770 Z= 0.103 Angle : 0.535 10.860 21430 Z= 0.269 Chirality : 0.042 0.428 2535 Planarity : 0.003 0.034 2664 Dihedral : 8.864 93.852 2421 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.09 % Allowed : 9.26 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1974 helix: 1.37 (0.21), residues: 685 sheet: -0.44 (0.32), residues: 293 loop : -1.61 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 656 HIS 0.004 0.001 HIS C 35 PHE 0.011 0.001 PHE E 686 TYR 0.015 0.001 TYR B 31 ARG 0.003 0.000 ARG D 417 Details of bonding type rmsd link_NAG-ASN : bond 0.00844 ( 9) link_NAG-ASN : angle 4.00111 ( 27) link_BETA1-4 : bond 0.00666 ( 5) link_BETA1-4 : angle 2.99820 ( 15) hydrogen bonds : bond 0.04402 ( 571) hydrogen bonds : angle 4.21551 ( 1662) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.48399 ( 10) covalent geometry : bond 0.00217 (15751) covalent geometry : angle 0.50966 (21378) *********************** 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 83 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 1.843 Fit side-chains REVERT: B 304 MET cc_start: 0.9288 (tpp) cc_final: 0.8815 (ttm) REVERT: B 389 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9323 (mt) REVERT: C 76 LYS cc_start: 0.9544 (mppt) cc_final: 0.9293 (mtmm) REVERT: D 366 MET cc_start: 0.8838 (mmm) cc_final: 0.7943 (mmm) REVERT: D 412 LEU cc_start: 0.9228 (mt) cc_final: 0.8944 (mp) REVERT: E 278 MET cc_start: 0.9110 (tmm) cc_final: 0.8085 (tmm) REVERT: E 374 MET cc_start: 0.9304 (ttm) cc_final: 0.8900 (ttm) REVERT: E 486 MET cc_start: 0.9379 (mmm) cc_final: 0.9110 (mmm) outliers start: 18 outliers final: 5 residues processed: 79 average time/residue: 0.2468 time to fit residues: 31.6891 Evaluate side-chains 67 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 74 TYR 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 127 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 5 optimal weight: 0.0000 chunk 194 optimal weight: 0.0270 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 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 = 0.3335 r_free = 0.3335 target = 0.054841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.035858 restraints weight = 78928.147| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 4.21 r_work: 0.2574 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15770 Z= 0.091 Angle : 0.518 10.455 21430 Z= 0.257 Chirality : 0.042 0.411 2535 Planarity : 0.003 0.033 2664 Dihedral : 8.192 91.825 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.03 % Allowed : 9.50 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1974 helix: 1.52 (0.21), residues: 695 sheet: -0.32 (0.33), residues: 286 loop : -1.57 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 656 HIS 0.004 0.000 HIS C 35 PHE 0.011 0.001 PHE E 686 TYR 0.017 0.001 TYR C 173 ARG 0.004 0.000 ARG E 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00806 ( 9) link_NAG-ASN : angle 3.80528 ( 27) link_BETA1-4 : bond 0.00616 ( 5) link_BETA1-4 : angle 2.98607 ( 15) hydrogen bonds : bond 0.03985 ( 571) hydrogen bonds : angle 4.01157 ( 1662) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.42847 ( 10) covalent geometry : bond 0.00189 (15751) covalent geometry : angle 0.49477 (21378) *********************** 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 86 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: B 304 MET cc_start: 0.9153 (tpp) cc_final: 0.8718 (ttm) REVERT: B 389 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9267 (mt) REVERT: C 76 LYS cc_start: 0.9563 (mppt) cc_final: 0.9254 (mtmm) REVERT: D 364 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8121 (t) REVERT: D 366 MET cc_start: 0.8760 (mmm) cc_final: 0.7971 (mmm) REVERT: D 381 PHE cc_start: 0.3908 (OUTLIER) cc_final: 0.3019 (t80) REVERT: E 278 MET cc_start: 0.9122 (tmm) cc_final: 0.8065 (tmm) REVERT: E 374 MET cc_start: 0.9319 (ttm) cc_final: 0.8917 (ttm) outliers start: 17 outliers final: 7 residues processed: 83 average time/residue: 0.2451 time to fit residues: 33.5164 Evaluate side-chains 71 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 651 CYS 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 99 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 190 optimal weight: 0.2980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3300 r_free = 0.3300 target = 0.053435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.034308 restraints weight = 78810.158| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 4.13 r_work: 0.2519 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15770 Z= 0.162 Angle : 0.565 10.964 21430 Z= 0.282 Chirality : 0.042 0.408 2535 Planarity : 0.003 0.032 2664 Dihedral : 7.978 91.210 2418 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.85 % Allowed : 10.41 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1974 helix: 1.61 (0.21), residues: 699 sheet: -0.35 (0.32), residues: 291 loop : -1.60 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 656 HIS 0.003 0.001 HIS D 489 PHE 0.014 0.001 PHE B 87 TYR 0.017 0.001 TYR C 173 ARG 0.002 0.000 ARG E 489 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 9) link_NAG-ASN : angle 3.76117 ( 27) link_BETA1-4 : bond 0.00541 ( 5) link_BETA1-4 : angle 2.89738 ( 15) hydrogen bonds : bond 0.04870 ( 571) hydrogen bonds : angle 4.13430 ( 1662) SS BOND : bond 0.00333 ( 5) SS BOND : angle 0.73218 ( 10) covalent geometry : bond 0.00373 (15751) covalent geometry : angle 0.54446 (21378) *********************** 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 76 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.832 Fit side-chains revert: symmetry clash REVERT: B 304 MET cc_start: 0.9140 (tpp) cc_final: 0.8837 (ttt) REVERT: B 389 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9226 (mt) REVERT: C 76 LYS cc_start: 0.9565 (mppt) cc_final: 0.9235 (mtmm) REVERT: D 364 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8205 (t) REVERT: D 366 MET cc_start: 0.8803 (mmm) cc_final: 0.8037 (mmm) REVERT: D 381 PHE cc_start: 0.4116 (OUTLIER) cc_final: 0.3016 (t80) REVERT: E 278 MET cc_start: 0.9108 (tmm) cc_final: 0.8069 (tmm) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.2432 time to fit residues: 29.4922 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 : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 165 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 77 optimal weight: 0.0060 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.053561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.034414 restraints weight = 78920.902| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 4.15 r_work: 0.2524 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15770 Z= 0.140 Angle : 0.545 10.722 21430 Z= 0.272 Chirality : 0.042 0.402 2535 Planarity : 0.003 0.033 2664 Dihedral : 7.575 89.174 2418 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.15 % Allowed : 10.34 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1974 helix: 1.68 (0.21), residues: 696 sheet: -0.43 (0.32), residues: 286 loop : -1.55 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 656 HIS 0.002 0.001 HIS E 674 PHE 0.012 0.001 PHE E 686 TYR 0.015 0.001 TYR B 31 ARG 0.002 0.000 ARG E 484 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 9) link_NAG-ASN : angle 3.62450 ( 27) link_BETA1-4 : bond 0.00595 ( 5) link_BETA1-4 : angle 2.87666 ( 15) hydrogen bonds : bond 0.04701 ( 571) hydrogen bonds : angle 4.07538 ( 1662) SS BOND : bond 0.00299 ( 5) SS BOND : angle 1.01910 ( 10) covalent geometry : bond 0.00321 (15751) covalent geometry : angle 0.52393 (21378) *********************** 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 82 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 1.733 Fit side-chains REVERT: A 290 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8937 (tt) REVERT: B 304 MET cc_start: 0.9062 (tpp) cc_final: 0.8829 (ttt) REVERT: B 389 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9195 (mt) REVERT: C 76 LYS cc_start: 0.9571 (mppt) cc_final: 0.9172 (mtmm) REVERT: D 364 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8157 (t) REVERT: D 366 MET cc_start: 0.8812 (mmm) cc_final: 0.8034 (mmm) REVERT: D 381 PHE cc_start: 0.4298 (OUTLIER) cc_final: 0.3081 (t80) REVERT: D 412 LEU cc_start: 0.9257 (mt) cc_final: 0.8971 (mp) REVERT: E 278 MET cc_start: 0.9117 (tmm) cc_final: 0.8102 (tmm) REVERT: E 486 MET cc_start: 0.9019 (mmt) cc_final: 0.8785 (mmm) outliers start: 19 outliers final: 9 residues processed: 79 average time/residue: 0.2470 time to fit residues: 31.8945 Evaluate side-chains 74 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 140 optimal weight: 20.0000 chunk 102 optimal weight: 0.4980 chunk 150 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.053666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.034603 restraints weight = 78211.343| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 4.13 r_work: 0.2531 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15770 Z= 0.128 Angle : 0.551 10.611 21430 Z= 0.273 Chirality : 0.042 0.401 2535 Planarity : 0.003 0.032 2664 Dihedral : 7.308 87.973 2418 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.91 % Allowed : 10.83 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.20), residues: 1974 helix: 1.78 (0.21), residues: 690 sheet: -0.33 (0.33), residues: 281 loop : -1.53 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 656 HIS 0.002 0.001 HIS E 674 PHE 0.012 0.001 PHE B 87 TYR 0.017 0.001 TYR C 173 ARG 0.002 0.000 ARG E 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 9) link_NAG-ASN : angle 3.56803 ( 27) link_BETA1-4 : bond 0.00599 ( 5) link_BETA1-4 : angle 2.86797 ( 15) hydrogen bonds : bond 0.04591 ( 571) hydrogen bonds : angle 4.03844 ( 1662) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.87524 ( 10) covalent geometry : bond 0.00291 (15751) covalent geometry : angle 0.53104 (21378) *********************** 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 77 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: A 290 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8929 (tt) REVERT: B 389 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9377 (mt) REVERT: C 76 LYS cc_start: 0.9574 (mppt) cc_final: 0.9170 (mtmm) REVERT: D 364 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8129 (t) REVERT: D 366 MET cc_start: 0.8805 (mmm) cc_final: 0.8064 (mmm) REVERT: D 381 PHE cc_start: 0.4144 (OUTLIER) cc_final: 0.3073 (t80) REVERT: E 278 MET cc_start: 0.9133 (tmm) cc_final: 0.8115 (tmm) REVERT: E 374 MET cc_start: 0.9356 (ttm) cc_final: 0.8911 (mtm) REVERT: E 486 MET cc_start: 0.9046 (mmt) cc_final: 0.8827 (mmm) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.2439 time to fit residues: 29.1741 Evaluate side-chains 75 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 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 79 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.054663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.035661 restraints weight = 78011.265| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 4.17 r_work: 0.2566 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15770 Z= 0.095 Angle : 0.521 10.143 21430 Z= 0.257 Chirality : 0.041 0.389 2535 Planarity : 0.003 0.034 2664 Dihedral : 6.840 85.840 2418 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.91 % Allowed : 10.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1974 helix: 1.82 (0.21), residues: 687 sheet: -0.16 (0.34), residues: 276 loop : -1.48 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 656 HIS 0.003 0.000 HIS C 35 PHE 0.011 0.001 PHE E 686 TYR 0.015 0.001 TYR B 31 ARG 0.002 0.000 ARG E 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 9) link_NAG-ASN : angle 3.46241 ( 27) link_BETA1-4 : bond 0.00621 ( 5) link_BETA1-4 : angle 2.84794 ( 15) hydrogen bonds : bond 0.03853 ( 571) hydrogen bonds : angle 3.87358 ( 1662) SS BOND : bond 0.00254 ( 5) SS BOND : angle 0.65656 ( 10) covalent geometry : bond 0.00205 (15751) covalent geometry : angle 0.50154 (21378) *********************** 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 78 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 290 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8842 (tt) REVERT: B 389 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9381 (mt) REVERT: C 76 LYS cc_start: 0.9591 (mppt) cc_final: 0.9271 (mtmm) REVERT: D 364 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8145 (t) REVERT: D 366 MET cc_start: 0.8804 (mmm) cc_final: 0.8013 (mmm) REVERT: D 381 PHE cc_start: 0.3898 (OUTLIER) cc_final: 0.2826 (t80) REVERT: E 278 MET cc_start: 0.9153 (tmm) cc_final: 0.8231 (tmm) REVERT: E 486 MET cc_start: 0.9039 (mmt) cc_final: 0.8819 (mmm) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.2543 time to fit residues: 31.0795 Evaluate side-chains 73 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 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 93 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.0050 chunk 151 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.4798 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.054313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.035241 restraints weight = 78549.330| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 4.18 r_work: 0.2552 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15770 Z= 0.110 Angle : 0.528 10.289 21430 Z= 0.260 Chirality : 0.041 0.390 2535 Planarity : 0.003 0.032 2664 Dihedral : 6.609 84.132 2418 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.73 % Allowed : 11.01 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1974 helix: 1.89 (0.21), residues: 686 sheet: -0.18 (0.34), residues: 276 loop : -1.46 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 656 HIS 0.003 0.000 HIS C 35 PHE 0.011 0.001 PHE B 87 TYR 0.015 0.001 TYR B 31 ARG 0.002 0.000 ARG B 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00693 ( 9) link_NAG-ASN : angle 3.42591 ( 27) link_BETA1-4 : bond 0.00623 ( 5) link_BETA1-4 : angle 2.81724 ( 15) hydrogen bonds : bond 0.04074 ( 571) hydrogen bonds : angle 3.87621 ( 1662) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.67960 ( 10) covalent geometry : bond 0.00248 (15751) covalent geometry : angle 0.50869 (21378) ********************** 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 73 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.822 Fit side-chains revert: symmetry clash REVERT: A 290 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8854 (tt) REVERT: B 389 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9354 (mt) REVERT: C 76 LYS cc_start: 0.9574 (mppt) cc_final: 0.9157 (mtmm) REVERT: D 364 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8150 (t) REVERT: D 366 MET cc_start: 0.8797 (mmm) cc_final: 0.8104 (mmm) REVERT: D 381 PHE cc_start: 0.4056 (OUTLIER) cc_final: 0.2992 (t80) REVERT: E 278 MET cc_start: 0.9144 (tmm) cc_final: 0.8113 (tmm) REVERT: E 486 MET cc_start: 0.9043 (mmt) cc_final: 0.8822 (mmm) outliers start: 12 outliers final: 8 residues processed: 70 average time/residue: 0.2504 time to fit residues: 28.7527 Evaluate side-chains 73 residues out of total 1669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 0.0060 chunk 128 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 180 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.054665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035671 restraints weight = 77600.956| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 4.16 r_work: 0.2569 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15770 Z= 0.096 Angle : 0.520 10.135 21430 Z= 0.255 Chirality : 0.041 0.387 2535 Planarity : 0.003 0.033 2664 Dihedral : 6.372 82.509 2418 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.85 % Allowed : 10.95 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1974 helix: 1.94 (0.21), residues: 684 sheet: -0.14 (0.34), residues: 276 loop : -1.46 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 656 HIS 0.003 0.000 HIS C 35 PHE 0.010 0.001 PHE B 87 TYR 0.015 0.001 TYR B 31 ARG 0.002 0.000 ARG E 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 9) link_NAG-ASN : angle 3.33746 ( 27) link_BETA1-4 : bond 0.00562 ( 5) link_BETA1-4 : angle 2.75527 ( 15) hydrogen bonds : bond 0.03848 ( 571) hydrogen bonds : angle 3.83643 ( 1662) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.61701 ( 10) covalent geometry : bond 0.00210 (15751) covalent geometry : angle 0.50117 (21378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7545.38 seconds wall clock time: 131 minutes 23.20 seconds (7883.20 seconds total)