Starting phenix.real_space_refine on Thu Feb 5 13:06:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8c_47716/02_2026/9e8c_47716.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8c_47716/02_2026/9e8c_47716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e8c_47716/02_2026/9e8c_47716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8c_47716/02_2026/9e8c_47716.map" model { file = "/net/cci-nas-00/data/ceres_data/9e8c_47716/02_2026/9e8c_47716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8c_47716/02_2026/9e8c_47716.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 Mg 2 5.21 5 S 111 5.16 5 C 10676 2.51 5 N 2911 2.21 5 O 3364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17076 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4525 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 37, 'TRANS': 557} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3762 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 464} Chain breaks: 7 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4599 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 37, 'TRANS': 564} Chain: "D" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3891 Classifications: {'peptide': 506} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 476} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "M" 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 46 Unusual residues: {' CA': 4, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' MG': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 46 Unusual residues: {' CA': 4, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' MG': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.62, per 1000 atoms: 0.27 Number of scatterers: 17076 At special positions: 0 Unit cell: (75.97, 148.73, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 S 111 16.00 Mg 2 11.99 O 3364 8.00 N 2911 7.00 C 10676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 198 " distance=2.02 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 461 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 515 " distance=2.03 Simple disulfide: pdb=" SG CYS C 521 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 461 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS D 258 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 400 " - pdb=" SG CYS D 412 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 459 " distance=2.03 Simple disulfide: pdb=" SG CYS D 463 " - pdb=" SG CYS D 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 486 " distance=2.02 Simple disulfide: pdb=" SG CYS D 488 " - pdb=" SG CYS D 497 " distance=2.03 Simple disulfide: pdb=" SG CYS D 512 " - pdb=" SG CYS D 521 " distance=1.89 Simple disulfide: pdb=" SG CYS D 512 " - pdb=" SG CYS D 527 " distance=2.15 Simple disulfide: pdb=" SG CYS D 512 " - pdb=" SG CYS D 532 " distance=2.05 Simple disulfide: pdb=" SG CYS D 521 " - pdb=" SG CYS D 527 " distance=2.04 Simple disulfide: pdb=" SG CYS D 521 " - pdb=" SG CYS D 532 " distance=2.14 Simple disulfide: pdb=" SG CYS D 527 " - pdb=" SG CYS D 532 " distance=1.89 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 E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG G 1 " - " NAG G 2 " " BMA H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A1105 " - " ASN A 280 " " NAG C1105 " - " ASN C 280 " " NAG E 1 " - " ASN B 346 " " NAG K 1 " - " ASN D 346 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 875.0 milliseconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4012 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 35 sheets defined 15.3% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.585A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 590 through 594 removed outlier: 4.267A pdb=" N LEU A 593 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 removed outlier: 4.568A pdb=" N SER B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.651A pdb=" N TRP B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 159 " --> pdb=" O TRP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 removed outlier: 4.542A pdb=" N LYS B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 removed outlier: 3.956A pdb=" N LEU B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.512A pdb=" N GLN B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.917A pdb=" N ALA B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.541A pdb=" N LYS B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.836A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 removed outlier: 3.734A pdb=" N ARG B 378 " --> pdb=" O TYR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 467 Processing helix chain 'C' and resid 182 through 189 removed outlier: 3.998A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'D' and resid 38 through 46 removed outlier: 3.508A pdb=" N LEU D 43 " --> pdb=" O CYS D 39 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 46 " --> pdb=" O CYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.640A pdb=" N LYS D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.537A pdb=" N SER D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.818A pdb=" N LYS D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.675A pdb=" N PHE D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 258 removed outlier: 3.905A pdb=" N ALA D 251 " --> pdb=" O GLY D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 284 through 290 removed outlier: 3.689A pdb=" N ARG D 287 " --> pdb=" O LEU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 365 through 379 Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 489 through 493 removed outlier: 3.964A pdb=" N LEU D 493 " --> pdb=" O PRO D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 528 through 532 removed outlier: 4.134A pdb=" N CYS D 532 " --> pdb=" O CYS D 529 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 58 removed outlier: 3.852A pdb=" N SER A 53 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 84 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.816A pdb=" N SER A 269 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS A 309 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 327 Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 395 removed outlier: 5.130A pdb=" N ASP A 404 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 436 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 518 through 525 Processing sheet with id=AB2, first strand: chain 'A' and resid 496 through 497 removed outlier: 4.058A pdb=" N LEU A 497 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 496 through 497 removed outlier: 4.058A pdb=" N LEU A 497 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AB5, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB6, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AB7, first strand: chain 'B' and resid 87 through 91 removed outlier: 6.318A pdb=" N ARG B 113 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 114 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 223 removed outlier: 6.875A pdb=" N VAL B 219 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA B 181 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR B 221 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE B 179 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL B 138 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLY B 178 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 140 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLY B 180 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR B 142 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE B 182 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N MET B 144 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 141 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE B 333 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 272 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 335 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE B 274 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR B 337 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR B 276 " --> pdb=" O THR B 337 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 40 through 43 removed outlier: 6.377A pdb=" N ASP C 465 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 455 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 451 " --> pdb=" O GLY C 469 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 54 through 58 Processing sheet with id=AC4, first strand: chain 'C' and resid 106 through 108 Processing sheet with id=AC5, first strand: chain 'C' and resid 128 through 131 Processing sheet with id=AC6, first strand: chain 'C' and resid 203 through 206 removed outlier: 3.720A pdb=" N SER C 203 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 270 through 273 Processing sheet with id=AC8, first strand: chain 'C' and resid 324 through 327 Processing sheet with id=AC9, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AD1, first strand: chain 'C' and resid 391 through 395 removed outlier: 6.052A pdb=" N ASP C 404 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 436 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 486 through 493 removed outlier: 3.568A pdb=" N GLN C 519 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 513 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 486 through 493 removed outlier: 3.568A pdb=" N GLN C 519 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 514 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 561 through 567 Processing sheet with id=AD5, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AD6, first strand: chain 'D' and resid 86 through 91 removed outlier: 6.544A pdb=" N ARG D 113 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE D 114 " --> pdb=" O GLN D 454 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR D 456 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU D 116 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 381 " --> pdb=" O CYS D 412 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 109 through 110 removed outlier: 4.055A pdb=" N PHE D 396 " --> pdb=" O GLY D 408 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 216 through 223 removed outlier: 6.339A pdb=" N PHE D 179 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N THR D 221 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE D 177 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP D 139 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL D 273 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR D 141 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR D 275 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU D 143 " --> pdb=" O THR D 275 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1311 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: 3.16 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5591 1.34 - 1.46: 3638 1.46 - 1.58: 8049 1.58 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 17422 Sorted by residual: bond pdb=" C1 NAG A1105 " pdb=" O5 NAG A1105 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N ARG B 505 " pdb=" CA ARG B 505 " ideal model delta sigma weight residual 1.456 1.488 -0.032 9.80e-03 1.04e+04 1.05e+01 bond pdb=" C1 NAG H 3 " pdb=" O5 NAG H 3 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" N GLN A 482 " pdb=" CA GLN A 482 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.18e-02 7.18e+03 9.53e+00 bond pdb=" N VAL A 484 " pdb=" CA VAL A 484 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.65e+00 ... (remaining 17417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 22901 1.71 - 3.42: 655 3.42 - 5.13: 95 5.13 - 6.84: 21 6.84 - 8.55: 5 Bond angle restraints: 23677 Sorted by residual: angle pdb=" N CYS B 512 " pdb=" CA CYS B 512 " pdb=" C CYS B 512 " ideal model delta sigma weight residual 112.38 105.85 6.53 1.22e+00 6.72e-01 2.87e+01 angle pdb=" N ASP B 285 " pdb=" CA ASP B 285 " pdb=" C ASP B 285 " ideal model delta sigma weight residual 111.82 107.19 4.63 1.16e+00 7.43e-01 1.60e+01 angle pdb=" N ASN D 478 " pdb=" CA ASN D 478 " pdb=" C ASN D 478 " ideal model delta sigma weight residual 112.88 108.05 4.83 1.29e+00 6.01e-01 1.40e+01 angle pdb=" CA CYS D 474 " pdb=" C CYS D 474 " pdb=" O CYS D 474 " ideal model delta sigma weight residual 122.37 118.16 4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" CA ASP A 396 " pdb=" C ASP A 396 " pdb=" O ASP A 396 " ideal model delta sigma weight residual 122.36 117.96 4.40 1.21e+00 6.83e-01 1.32e+01 ... (remaining 23672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 10259 24.85 - 49.71: 424 49.71 - 74.56: 71 74.56 - 99.41: 40 99.41 - 124.27: 31 Dihedral angle restraints: 10825 sinusoidal: 4558 harmonic: 6267 Sorted by residual: dihedral pdb=" CB CYS D 512 " pdb=" SG CYS D 512 " pdb=" SG CYS D 521 " pdb=" CB CYS D 521 " ideal model delta sinusoidal sigma weight residual 93.00 9.96 83.04 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS D 463 " pdb=" SG CYS D 463 " pdb=" SG CYS D 483 " pdb=" CB CYS D 483 " ideal model delta sinusoidal sigma weight residual 93.00 175.45 -82.45 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS D 527 " pdb=" SG CYS D 527 " pdb=" SG CYS D 532 " pdb=" CB CYS D 532 " ideal model delta sinusoidal sigma weight residual 93.00 20.85 72.15 1 1.00e+01 1.00e-02 6.66e+01 ... (remaining 10822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2080 0.053 - 0.107: 499 0.107 - 0.160: 96 0.160 - 0.213: 2 0.213 - 0.267: 3 Chirality restraints: 2680 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.61e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2677 not shown) Planarity restraints: 3107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 515 " -0.321 9.50e-02 1.11e+02 1.44e-01 1.27e+01 pdb=" NE ARG B 515 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 515 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 515 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 515 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 473 " -0.317 9.50e-02 1.11e+02 1.42e-01 1.24e+01 pdb=" NE ARG D 473 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 473 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 473 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 473 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 453 " 0.191 9.50e-02 1.11e+02 8.55e-02 4.49e+00 pdb=" NE ARG C 453 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 453 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 453 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 453 " 0.007 2.00e-02 2.50e+03 ... (remaining 3104 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 364 2.62 - 3.19: 16120 3.19 - 3.76: 28357 3.76 - 4.33: 39763 4.33 - 4.90: 62893 Nonbonded interactions: 147497 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb="MG MG B 801 " model vdw 2.054 2.170 nonbonded pdb=" OD1 ASP A 465 " pdb="CA CA A1104 " model vdw 2.055 2.510 nonbonded pdb=" OD1 ASN C 461 " pdb="CA CA C1104 " model vdw 2.182 2.510 nonbonded pdb=" O THR C 281 " pdb="CA CA C1102 " model vdw 2.191 2.510 nonbonded pdb=" O VAL A 602 " pdb=" OG1 THR A 621 " model vdw 2.198 3.040 ... (remaining 147492 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' selection = (chain 'C' and (resid 32 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O or name CB )) or resid 168 through 348 or resid 353 through 531 or \ (resid 532 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 3 through 583 or (resid 584 and (name N or name CA or name C or name O or name C \ B )) or resid 585 through 589 or (resid 590 and (name N or name CA or name C or \ name O or name CB )) or resid 591 through 607 or (resid 611 through 612 and (nam \ e N or name CA or name C or name O or name CB )) or resid 613 through 1107)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 27 through 33 or resid 37 through 58 or resid 61 through 6 \ 2 or (resid 63 and (name N or name CA or name C or name O or name CB )) or resid \ 64 through 71 or (resid 72 and (name N or name CA or name C or name O or name C \ B )) or resid 73 through 379 or resid 381 through 390 or resid 392 through 429 o \ r resid 431 through 434 or (resid 435 and (name N or name CA or name C or name O \ or name CB )) or resid 436 through 475 or (resid 476 and (name N or name CA or \ name C or name O or name CB )) or resid 477 through 504 or (resid 505 and (name \ N or name CA or name C or name O or name CB )) or resid 506 or (resid 509 and (n \ ame N or name CA or name C or name O or name CB )) or resid 510 through 515 or ( \ resid 516 and (name N or name CA or name C or name O or name CB )) or resid 520 \ through 804)) } ncs_group { reference = (chain 'E' and resid 2) selection = (chain 'H' and resid 2) selection = (chain 'K' and resid 2) } ncs_group { reference = chain 'G' selection = chain 'M' } 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.930 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 17472 Z= 0.256 Angle : 0.850 30.282 23789 Z= 0.450 Chirality : 0.048 0.267 2680 Planarity : 0.006 0.144 3103 Dihedral : 16.020 124.267 6699 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.19 % Favored : 92.49 % Rotamer: Outliers : 4.59 % Allowed : 10.69 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.18), residues: 2170 helix: -1.16 (0.30), residues: 265 sheet: -0.54 (0.20), residues: 648 loop : -1.71 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 310 TYR 0.012 0.001 TYR D 204 PHE 0.013 0.001 PHE A 582 TRP 0.017 0.001 TRP C 266 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00403 (17422) covalent geometry : angle 0.68632 (23677) SS BOND : bond 0.04211 ( 38) SS BOND : angle 8.55803 ( 76) hydrogen bonds : bond 0.16035 ( 496) hydrogen bonds : angle 8.44770 ( 1311) link_BETA1-4 : bond 0.01259 ( 8) link_BETA1-4 : angle 4.22195 ( 24) link_NAG-ASN : bond 0.00505 ( 4) link_NAG-ASN : angle 1.86066 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 132 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7338 (p90) REVERT: A 251 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7923 (p) REVERT: A 307 ARG cc_start: 0.6112 (ttp-110) cc_final: 0.5871 (ttp-110) REVERT: A 518 ILE cc_start: 0.8610 (mp) cc_final: 0.8397 (OUTLIER) REVERT: B 100 SER cc_start: 0.8313 (m) cc_final: 0.7741 (m) REVERT: B 105 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8136 (tm-30) REVERT: B 231 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 374 TYR cc_start: 0.8472 (t80) cc_final: 0.8203 (t80) REVERT: C 106 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7062 (mt-10) REVERT: C 319 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: C 518 ILE cc_start: 0.7869 (mt) cc_final: 0.7624 (mp) REVERT: C 555 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6405 (mp) REVERT: C 576 CYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4722 (m) REVERT: D 48 MET cc_start: 0.9097 (tpt) cc_final: 0.8859 (tpt) REVERT: D 382 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7334 (tm-30) outliers start: 85 outliers final: 28 residues processed: 210 average time/residue: 0.4635 time to fit residues: 111.7540 Evaluate side-chains 130 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain D residue 527 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 0.2980 chunk 212 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 531 GLN A 577 HIS B 129 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 189 ASN C 475 GLN C 527 HIS D 40 GLN D 129 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.079158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.059383 restraints weight = 63670.868| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.29 r_work: 0.3276 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 17472 Z= 0.254 Angle : 0.884 33.853 23789 Z= 0.430 Chirality : 0.048 0.202 2680 Planarity : 0.004 0.038 3103 Dihedral : 13.112 110.981 2858 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.71 % Favored : 91.06 % Rotamer: Outliers : 4.70 % Allowed : 13.55 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.18), residues: 2170 helix: -1.24 (0.30), residues: 267 sheet: -0.65 (0.20), residues: 658 loop : -1.80 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 169 TYR 0.023 0.002 TYR D 204 PHE 0.017 0.002 PHE A 448 TRP 0.018 0.002 TRP C 266 HIS 0.005 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00539 (17422) covalent geometry : angle 0.71735 (23677) SS BOND : bond 0.04343 ( 38) SS BOND : angle 8.84156 ( 76) hydrogen bonds : bond 0.04152 ( 496) hydrogen bonds : angle 7.47713 ( 1311) link_BETA1-4 : bond 0.01041 ( 8) link_BETA1-4 : angle 4.06193 ( 24) link_NAG-ASN : bond 0.00579 ( 4) link_NAG-ASN : angle 2.45586 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 107 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7508 (tpp80) REVERT: A 197 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7231 (p90) REVERT: A 251 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7903 (p) REVERT: A 307 ARG cc_start: 0.6205 (ttp-110) cc_final: 0.5925 (ttp-110) REVERT: A 316 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.5761 (ttm) REVERT: A 335 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.6897 (m90) REVERT: A 518 ILE cc_start: 0.8762 (mp) cc_final: 0.8551 (OUTLIER) REVERT: B 100 SER cc_start: 0.8386 (m) cc_final: 0.7888 (m) REVERT: B 105 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8125 (tm-30) REVERT: B 253 MET cc_start: 0.6236 (tpt) cc_final: 0.6028 (tpt) REVERT: B 330 ILE cc_start: 0.8482 (mt) cc_final: 0.7987 (mm) REVERT: B 374 TYR cc_start: 0.8485 (t80) cc_final: 0.8172 (t80) REVERT: B 419 ASP cc_start: 0.6747 (m-30) cc_final: 0.6511 (m-30) REVERT: C 106 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7140 (mt-10) REVERT: C 319 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8030 (m-10) REVERT: C 575 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7221 (mp) REVERT: C 576 CYS cc_start: 0.5691 (OUTLIER) cc_final: 0.5192 (m) REVERT: D 48 MET cc_start: 0.9270 (tpt) cc_final: 0.8940 (tpt) outliers start: 87 outliers final: 36 residues processed: 178 average time/residue: 0.4080 time to fit residues: 84.5461 Evaluate side-chains 140 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 527 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 3 optimal weight: 0.0010 chunk 164 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.079580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.060034 restraints weight = 63755.252| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.30 r_work: 0.3298 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 17472 Z= 0.190 Angle : 0.850 31.664 23789 Z= 0.407 Chirality : 0.047 0.190 2680 Planarity : 0.004 0.047 3103 Dihedral : 10.892 110.528 2833 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.87 % Favored : 92.90 % Rotamer: Outliers : 4.10 % Allowed : 14.15 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.18), residues: 2170 helix: -1.05 (0.30), residues: 261 sheet: -0.66 (0.20), residues: 652 loop : -1.73 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 169 TYR 0.015 0.001 TYR A 471 PHE 0.016 0.002 PHE C 582 TRP 0.020 0.001 TRP C 266 HIS 0.005 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00375 (17422) covalent geometry : angle 0.68050 (23677) SS BOND : bond 0.04129 ( 38) SS BOND : angle 8.71317 ( 76) hydrogen bonds : bond 0.03654 ( 496) hydrogen bonds : angle 7.09660 ( 1311) link_BETA1-4 : bond 0.01120 ( 8) link_BETA1-4 : angle 4.08429 ( 24) link_NAG-ASN : bond 0.00472 ( 4) link_NAG-ASN : angle 2.30557 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 110 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7557 (m-30) cc_final: 0.7331 (m-30) REVERT: A 197 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7210 (p90) REVERT: A 251 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.7891 (p) REVERT: A 307 ARG cc_start: 0.6145 (ttp-110) cc_final: 0.5862 (ttp-110) REVERT: A 518 ILE cc_start: 0.8710 (mp) cc_final: 0.8469 (mp) REVERT: B 100 SER cc_start: 0.8374 (m) cc_final: 0.7886 (m) REVERT: B 105 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8106 (tm-30) REVERT: B 231 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7415 (pp20) REVERT: B 232 GLU cc_start: 0.7281 (tp30) cc_final: 0.6762 (tp30) REVERT: B 330 ILE cc_start: 0.8502 (mt) cc_final: 0.8026 (mm) REVERT: B 374 TYR cc_start: 0.8456 (t80) cc_final: 0.8170 (t80) REVERT: B 419 ASP cc_start: 0.6726 (m-30) cc_final: 0.6487 (m-30) REVERT: C 106 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7086 (mt-10) REVERT: C 319 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: C 575 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7493 (mp) REVERT: C 576 CYS cc_start: 0.5636 (OUTLIER) cc_final: 0.5180 (m) REVERT: D 48 MET cc_start: 0.9320 (tpt) cc_final: 0.9014 (tpt) REVERT: D 150 MET cc_start: 0.7792 (mmm) cc_final: 0.7124 (mmm) REVERT: D 382 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7671 (tm-30) outliers start: 76 outliers final: 35 residues processed: 173 average time/residue: 0.4826 time to fit residues: 96.8837 Evaluate side-chains 142 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 527 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 164 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 212 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 309 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.078314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.059168 restraints weight = 64410.670| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.30 r_work: 0.3250 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 17472 Z= 0.294 Angle : 0.880 30.636 23789 Z= 0.426 Chirality : 0.048 0.199 2680 Planarity : 0.004 0.048 3103 Dihedral : 9.574 109.392 2829 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.99 % Favored : 90.78 % Rotamer: Outliers : 4.70 % Allowed : 15.12 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.17), residues: 2170 helix: -1.22 (0.30), residues: 263 sheet: -0.72 (0.20), residues: 650 loop : -1.84 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 433 TYR 0.014 0.002 TYR B 204 PHE 0.017 0.002 PHE A 448 TRP 0.019 0.002 TRP C 266 HIS 0.008 0.001 HIS C 577 Details of bonding type rmsd covalent geometry : bond 0.00636 (17422) covalent geometry : angle 0.72220 (23677) SS BOND : bond 0.04279 ( 38) SS BOND : angle 8.58576 ( 76) hydrogen bonds : bond 0.03984 ( 496) hydrogen bonds : angle 7.18849 ( 1311) link_BETA1-4 : bond 0.01000 ( 8) link_BETA1-4 : angle 4.07764 ( 24) link_NAG-ASN : bond 0.00653 ( 4) link_NAG-ASN : angle 2.73484 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 102 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7679 (tpp80) cc_final: 0.7347 (tpp80) REVERT: A 251 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.7889 (p) REVERT: A 316 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.5703 (ttm) REVERT: A 335 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.6955 (m90) REVERT: A 518 ILE cc_start: 0.8762 (mp) cc_final: 0.8557 (mp) REVERT: B 100 SER cc_start: 0.8395 (m) cc_final: 0.7805 (m) REVERT: B 105 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8153 (tm-30) REVERT: B 231 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 349 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: B 374 TYR cc_start: 0.8458 (t80) cc_final: 0.8211 (t80) REVERT: B 419 ASP cc_start: 0.6833 (m-30) cc_final: 0.6565 (m-30) REVERT: C 319 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8227 (m-10) REVERT: C 576 CYS cc_start: 0.5648 (OUTLIER) cc_final: 0.5223 (m) REVERT: D 48 MET cc_start: 0.9320 (tpt) cc_final: 0.9018 (tpt) REVERT: D 191 MET cc_start: 0.8535 (ttp) cc_final: 0.8296 (ttp) REVERT: D 382 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7722 (tm-30) outliers start: 87 outliers final: 42 residues processed: 174 average time/residue: 0.4497 time to fit residues: 91.7142 Evaluate side-chains 145 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 527 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 211 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 309 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.080243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.060485 restraints weight = 62874.352| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.31 r_work: 0.3309 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 17472 Z= 0.170 Angle : 0.837 30.328 23789 Z= 0.398 Chirality : 0.046 0.211 2680 Planarity : 0.004 0.045 3103 Dihedral : 8.126 109.470 2824 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.54 % Favored : 93.23 % Rotamer: Outliers : 3.89 % Allowed : 16.36 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.18), residues: 2170 helix: -0.96 (0.31), residues: 256 sheet: -0.64 (0.20), residues: 647 loop : -1.72 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 590 TYR 0.012 0.001 TYR A 197 PHE 0.015 0.001 PHE A 448 TRP 0.021 0.001 TRP C 266 HIS 0.004 0.001 HIS C 577 Details of bonding type rmsd covalent geometry : bond 0.00308 (17422) covalent geometry : angle 0.67289 (23677) SS BOND : bond 0.04407 ( 38) SS BOND : angle 8.48687 ( 76) hydrogen bonds : bond 0.03289 ( 496) hydrogen bonds : angle 6.82731 ( 1311) link_BETA1-4 : bond 0.01108 ( 8) link_BETA1-4 : angle 4.05855 ( 24) link_NAG-ASN : bond 0.00443 ( 4) link_NAG-ASN : angle 2.27493 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 104 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7455 (m-30) cc_final: 0.7137 (m-30) REVERT: A 121 ARG cc_start: 0.7566 (tpp80) cc_final: 0.7321 (tpp80) REVERT: A 335 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.6995 (m90) REVERT: A 345 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6775 (mmm) REVERT: A 518 ILE cc_start: 0.8715 (mp) cc_final: 0.8504 (mp) REVERT: B 100 SER cc_start: 0.8393 (m) cc_final: 0.8133 (m) REVERT: B 105 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8422 (tp40) REVERT: B 330 ILE cc_start: 0.8493 (mt) cc_final: 0.8000 (mm) REVERT: B 349 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: B 374 TYR cc_start: 0.8471 (t80) cc_final: 0.8219 (t80) REVERT: C 106 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7056 (mt-10) REVERT: C 319 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8284 (m-10) REVERT: C 575 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7218 (mp) REVERT: C 576 CYS cc_start: 0.5512 (OUTLIER) cc_final: 0.5059 (m) REVERT: D 48 MET cc_start: 0.9282 (tpt) cc_final: 0.8999 (tpt) REVERT: D 150 MET cc_start: 0.7769 (mmm) cc_final: 0.7230 (mmm) REVERT: D 191 MET cc_start: 0.8528 (ttp) cc_final: 0.8259 (ttp) REVERT: D 382 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7696 (tm-30) outliers start: 72 outliers final: 29 residues processed: 166 average time/residue: 0.4728 time to fit residues: 91.1373 Evaluate side-chains 130 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 527 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 185 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 309 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.079350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.059465 restraints weight = 63332.645| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.30 r_work: 0.3283 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 17472 Z= 0.222 Angle : 0.840 28.441 23789 Z= 0.402 Chirality : 0.046 0.218 2680 Planarity : 0.004 0.040 3103 Dihedral : 7.397 108.245 2817 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.97 % Favored : 91.80 % Rotamer: Outliers : 3.62 % Allowed : 16.95 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.18), residues: 2170 helix: -0.97 (0.30), residues: 267 sheet: -0.68 (0.20), residues: 657 loop : -1.75 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 366 TYR 0.017 0.001 TYR D 204 PHE 0.016 0.002 PHE A 448 TRP 0.019 0.002 TRP C 266 HIS 0.005 0.001 HIS C 577 Details of bonding type rmsd covalent geometry : bond 0.00446 (17422) covalent geometry : angle 0.68270 (23677) SS BOND : bond 0.04656 ( 38) SS BOND : angle 8.33526 ( 76) hydrogen bonds : bond 0.03431 ( 496) hydrogen bonds : angle 6.81319 ( 1311) link_BETA1-4 : bond 0.01028 ( 8) link_BETA1-4 : angle 4.01693 ( 24) link_NAG-ASN : bond 0.00520 ( 4) link_NAG-ASN : angle 2.56176 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 102 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7552 (m-30) cc_final: 0.7327 (m-30) REVERT: A 121 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7354 (tpp80) REVERT: A 197 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.7241 (p90) REVERT: A 335 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.6984 (m90) REVERT: A 345 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6666 (mmm) REVERT: A 518 ILE cc_start: 0.8644 (mp) cc_final: 0.8404 (mp) REVERT: B 100 SER cc_start: 0.8324 (m) cc_final: 0.7786 (m) REVERT: B 105 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8147 (tm-30) REVERT: B 231 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8347 (mm-30) REVERT: B 330 ILE cc_start: 0.8564 (mt) cc_final: 0.8076 (mm) REVERT: B 349 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: B 374 TYR cc_start: 0.8474 (t80) cc_final: 0.8160 (t80) REVERT: C 106 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7084 (mt-10) REVERT: C 319 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: C 576 CYS cc_start: 0.5616 (OUTLIER) cc_final: 0.5178 (m) REVERT: D 48 MET cc_start: 0.9277 (tpt) cc_final: 0.8998 (tpt) REVERT: D 191 MET cc_start: 0.8517 (ttp) cc_final: 0.8208 (ttp) outliers start: 67 outliers final: 36 residues processed: 161 average time/residue: 0.4464 time to fit residues: 83.8327 Evaluate side-chains 137 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 163 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 309 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.079310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.059498 restraints weight = 63186.444| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.31 r_work: 0.3280 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 17472 Z= 0.232 Angle : 0.828 27.271 23789 Z= 0.397 Chirality : 0.046 0.236 2680 Planarity : 0.004 0.038 3103 Dihedral : 7.169 108.196 2816 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.51 % Favored : 92.26 % Rotamer: Outliers : 4.10 % Allowed : 17.12 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.18), residues: 2170 helix: -0.93 (0.31), residues: 258 sheet: -0.64 (0.20), residues: 649 loop : -1.73 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 366 TYR 0.019 0.001 TYR D 204 PHE 0.015 0.002 PHE A 448 TRP 0.019 0.002 TRP C 266 HIS 0.005 0.001 HIS C 577 Details of bonding type rmsd covalent geometry : bond 0.00449 (17422) covalent geometry : angle 0.68214 (23677) SS BOND : bond 0.05420 ( 38) SS BOND : angle 8.00086 ( 76) hydrogen bonds : bond 0.03419 ( 496) hydrogen bonds : angle 6.80087 ( 1311) link_BETA1-4 : bond 0.00989 ( 8) link_BETA1-4 : angle 3.91977 ( 24) link_NAG-ASN : bond 0.00522 ( 4) link_NAG-ASN : angle 2.47237 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 103 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: A 197 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7058 (p90) REVERT: A 335 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.6987 (m90) REVERT: A 345 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6549 (mmm) REVERT: A 518 ILE cc_start: 0.8685 (mp) cc_final: 0.8417 (mp) REVERT: B 100 SER cc_start: 0.8344 (m) cc_final: 0.7777 (m) REVERT: B 105 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8048 (tm-30) REVERT: B 143 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6059 (mp) REVERT: B 330 ILE cc_start: 0.8594 (mt) cc_final: 0.8104 (mm) REVERT: B 332 LEU cc_start: 0.7595 (tt) cc_final: 0.7317 (tt) REVERT: B 349 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: B 374 TYR cc_start: 0.8471 (t80) cc_final: 0.8166 (t80) REVERT: C 106 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7062 (mt-10) REVERT: C 319 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: C 576 CYS cc_start: 0.5817 (OUTLIER) cc_final: 0.5381 (m) REVERT: D 48 MET cc_start: 0.9295 (tpt) cc_final: 0.9016 (tpt) REVERT: D 191 MET cc_start: 0.8524 (ttp) cc_final: 0.8232 (ttp) outliers start: 76 outliers final: 40 residues processed: 167 average time/residue: 0.4074 time to fit residues: 79.5174 Evaluate side-chains 146 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 211 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 309 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.080393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.060687 restraints weight = 63028.813| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.33 r_work: 0.3315 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 17472 Z= 0.182 Angle : 0.825 27.362 23789 Z= 0.391 Chirality : 0.045 0.208 2680 Planarity : 0.004 0.040 3103 Dihedral : 6.955 107.609 2816 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.82 % Favored : 92.95 % Rotamer: Outliers : 3.40 % Allowed : 17.76 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.18), residues: 2170 helix: -0.67 (0.31), residues: 256 sheet: -0.55 (0.20), residues: 650 loop : -1.61 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 366 TYR 0.018 0.001 TYR D 204 PHE 0.015 0.001 PHE A 582 TRP 0.020 0.001 TRP C 266 HIS 0.011 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00298 (17422) covalent geometry : angle 0.68115 (23677) SS BOND : bond 0.05457 ( 38) SS BOND : angle 7.96016 ( 76) hydrogen bonds : bond 0.03123 ( 496) hydrogen bonds : angle 6.60066 ( 1311) link_BETA1-4 : bond 0.00948 ( 8) link_BETA1-4 : angle 3.78666 ( 24) link_NAG-ASN : bond 0.00454 ( 4) link_NAG-ASN : angle 2.27119 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 104 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7676 (m-30) cc_final: 0.7379 (m-30) REVERT: A 197 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7151 (p90) REVERT: A 335 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.6984 (m90) REVERT: A 345 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6588 (mmm) REVERT: A 518 ILE cc_start: 0.8696 (mp) cc_final: 0.8385 (mp) REVERT: A 580 MET cc_start: 0.7063 (tpp) cc_final: 0.6311 (tpt) REVERT: B 100 SER cc_start: 0.8471 (m) cc_final: 0.8226 (m) REVERT: B 105 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8395 (tp40) REVERT: B 330 ILE cc_start: 0.8532 (mt) cc_final: 0.8027 (mm) REVERT: B 332 LEU cc_start: 0.7541 (tt) cc_final: 0.7262 (tt) REVERT: B 349 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: B 374 TYR cc_start: 0.8407 (t80) cc_final: 0.8118 (t80) REVERT: C 106 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7158 (mt-10) REVERT: C 319 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8370 (m-10) REVERT: C 575 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7221 (mp) REVERT: C 576 CYS cc_start: 0.5681 (OUTLIER) cc_final: 0.5230 (m) REVERT: D 48 MET cc_start: 0.9307 (tpt) cc_final: 0.9053 (tpt) outliers start: 63 outliers final: 34 residues processed: 157 average time/residue: 0.4151 time to fit residues: 76.6400 Evaluate side-chains 138 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 115 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 101 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 309 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS D 518 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.080966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.061175 restraints weight = 63117.190| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.36 r_work: 0.3328 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 17472 Z= 0.178 Angle : 0.818 27.611 23789 Z= 0.386 Chirality : 0.045 0.244 2680 Planarity : 0.004 0.041 3103 Dihedral : 6.729 106.436 2816 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.59 % Favored : 93.18 % Rotamer: Outliers : 2.65 % Allowed : 18.74 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.18), residues: 2170 helix: -0.38 (0.32), residues: 250 sheet: -0.48 (0.20), residues: 648 loop : -1.55 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 366 TYR 0.014 0.001 TYR D 204 PHE 0.014 0.001 PHE A 448 TRP 0.020 0.001 TRP C 266 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00289 (17422) covalent geometry : angle 0.67527 (23677) SS BOND : bond 0.05525 ( 38) SS BOND : angle 7.90989 ( 76) hydrogen bonds : bond 0.03028 ( 496) hydrogen bonds : angle 6.43036 ( 1311) link_BETA1-4 : bond 0.00862 ( 8) link_BETA1-4 : angle 3.51237 ( 24) link_NAG-ASN : bond 0.00439 ( 4) link_NAG-ASN : angle 2.22267 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 102 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7722 (m-30) cc_final: 0.7489 (m-30) REVERT: A 197 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.7055 (p90) REVERT: A 335 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.6944 (m90) REVERT: A 516 PHE cc_start: 0.5245 (p90) cc_final: 0.4680 (p90) REVERT: A 518 ILE cc_start: 0.8740 (mp) cc_final: 0.8428 (mp) REVERT: A 580 MET cc_start: 0.7137 (tpp) cc_final: 0.6391 (tpt) REVERT: B 100 SER cc_start: 0.8429 (m) cc_final: 0.7899 (m) REVERT: B 105 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8018 (tm-30) REVERT: B 330 ILE cc_start: 0.8513 (mt) cc_final: 0.8008 (mm) REVERT: B 332 LEU cc_start: 0.7521 (tt) cc_final: 0.7237 (tt) REVERT: B 349 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: B 374 TYR cc_start: 0.8396 (t80) cc_final: 0.8131 (t80) REVERT: C 106 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7175 (mt-10) REVERT: C 319 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: C 575 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7456 (mp) REVERT: C 576 CYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5137 (m) REVERT: D 48 MET cc_start: 0.9318 (tpt) cc_final: 0.9014 (tpt) outliers start: 49 outliers final: 32 residues processed: 144 average time/residue: 0.4721 time to fit residues: 78.5791 Evaluate side-chains 137 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 622 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 92 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 191 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 309 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.080537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.060832 restraints weight = 62464.251| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.32 r_work: 0.3319 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 17472 Z= 0.194 Angle : 0.824 27.606 23789 Z= 0.390 Chirality : 0.045 0.246 2680 Planarity : 0.004 0.043 3103 Dihedral : 6.705 106.067 2816 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.10 % Favored : 92.67 % Rotamer: Outliers : 2.43 % Allowed : 19.28 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2170 helix: -0.36 (0.33), residues: 250 sheet: -0.45 (0.21), residues: 648 loop : -1.57 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 366 TYR 0.011 0.001 TYR A 197 PHE 0.014 0.001 PHE A 448 TRP 0.019 0.002 TRP B 492 HIS 0.008 0.001 HIS C 622 Details of bonding type rmsd covalent geometry : bond 0.00339 (17422) covalent geometry : angle 0.68404 (23677) SS BOND : bond 0.05537 ( 38) SS BOND : angle 7.90089 ( 76) hydrogen bonds : bond 0.03080 ( 496) hydrogen bonds : angle 6.42601 ( 1311) link_BETA1-4 : bond 0.00766 ( 8) link_BETA1-4 : angle 3.37595 ( 24) link_NAG-ASN : bond 0.00453 ( 4) link_NAG-ASN : angle 2.26821 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7647 (m-30) cc_final: 0.7375 (m-30) REVERT: A 197 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.7150 (p90) REVERT: A 335 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.6977 (m90) REVERT: A 345 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6555 (mmm) REVERT: A 516 PHE cc_start: 0.5266 (p90) cc_final: 0.4714 (p90) REVERT: A 518 ILE cc_start: 0.8710 (mp) cc_final: 0.8395 (mp) REVERT: A 580 MET cc_start: 0.7163 (tpp) cc_final: 0.6485 (tpt) REVERT: B 100 SER cc_start: 0.8424 (m) cc_final: 0.7921 (m) REVERT: B 105 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8010 (tm-30) REVERT: B 148 TYR cc_start: 0.8288 (t80) cc_final: 0.7817 (m-80) REVERT: B 330 ILE cc_start: 0.8546 (mt) cc_final: 0.8039 (mm) REVERT: B 332 LEU cc_start: 0.7536 (tt) cc_final: 0.7186 (tt) REVERT: B 349 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: B 374 TYR cc_start: 0.8410 (t80) cc_final: 0.8157 (t80) REVERT: C 106 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7091 (mt-10) REVERT: C 319 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8512 (m-10) REVERT: C 575 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7499 (mp) REVERT: C 576 CYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5319 (m) REVERT: D 48 MET cc_start: 0.9317 (tpt) cc_final: 0.9095 (tpt) outliers start: 45 outliers final: 32 residues processed: 139 average time/residue: 0.4774 time to fit residues: 77.4090 Evaluate side-chains 135 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 42 optimal weight: 0.1980 chunk 129 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.080489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.060665 restraints weight = 62888.430| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.35 r_work: 0.3315 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 17472 Z= 0.194 Angle : 0.824 27.651 23789 Z= 0.390 Chirality : 0.045 0.237 2680 Planarity : 0.004 0.043 3103 Dihedral : 6.678 105.914 2816 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.00 % Favored : 92.86 % Rotamer: Outliers : 2.59 % Allowed : 19.22 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2170 helix: -0.40 (0.32), residues: 256 sheet: -0.44 (0.21), residues: 648 loop : -1.57 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 366 TYR 0.012 0.001 TYR D 204 PHE 0.026 0.001 PHE B 334 TRP 0.017 0.002 TRP C 266 HIS 0.011 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00339 (17422) covalent geometry : angle 0.68424 (23677) SS BOND : bond 0.05542 ( 38) SS BOND : angle 7.89511 ( 76) hydrogen bonds : bond 0.03097 ( 496) hydrogen bonds : angle 6.43551 ( 1311) link_BETA1-4 : bond 0.00730 ( 8) link_BETA1-4 : angle 3.30165 ( 24) link_NAG-ASN : bond 0.00455 ( 4) link_NAG-ASN : angle 2.26421 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5638.25 seconds wall clock time: 97 minutes 3.80 seconds (5823.80 seconds total)