Starting phenix.real_space_refine on Sat May 17 23:26:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsd_43494/05_2025/8vsd_43494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsd_43494/05_2025/8vsd_43494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vsd_43494/05_2025/8vsd_43494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsd_43494/05_2025/8vsd_43494.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsd_43494/05_2025/8vsd_43494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsd_43494/05_2025/8vsd_43494.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.059 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 5 9.91 5 Mg 1 5.21 5 S 83 5.16 5 C 10288 2.51 5 N 2813 2.21 5 O 3086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16276 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3950 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 29, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 86 Chain: "A" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4242 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 564} Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 200 Chain: "B" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2744 Classifications: {'peptide': 349} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "E" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2555 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 296} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2553 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.80, per 1000 atoms: 0.66 Number of scatterers: 16276 At special positions: 0 Unit cell: (100.981, 118.594, 237.188, 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 5 19.99 S 83 16.00 Mg 1 11.99 O 3086 8.00 N 2813 7.00 C 10288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 35 " distance=2.03 Simple disulfide: pdb=" SG CYS I 211 " - pdb=" SG CYS F 4 " distance=2.03 Simple disulfide: pdb=" SG CYS I 350 " - pdb=" SG CYS E 4 " distance=2.03 Simple disulfide: pdb=" SG CYS I 425 " - pdb=" SG CYS I 436 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 194 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 264 " - pdb=" SG CYS E 327 " distance=2.03 Simple disulfide: pdb=" SG CYS E 293 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 360 " distance=2.03 Simple disulfide: pdb=" SG CYS E 326 " - pdb=" SG CYS F 326 " distance=2.03 Simple disulfide: pdb=" SG CYS F 264 " - pdb=" SG CYS F 327 " distance=2.03 Simple disulfide: pdb=" SG CYS F 293 " - pdb=" SG CYS F 358 " distance=2.02 Simple disulfide: pdb=" SG CYS F 297 " - pdb=" SG CYS F 360 " distance=2.03 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 ALPHA1-2 " MAN C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 260 " " NAG B 501 " - " ASN B 360 " " NAG B 502 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG D 1 " - " ASN A 44 " " NAG G 1 " - " ASN B 191 " " NAG H 1 " - " ASN B 389 " " NAG J 1 " - " ASN B 414 " Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 2.0 seconds 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3928 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 31 sheets defined 16.2% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'I' and resid 65 through 71 removed outlier: 3.823A pdb=" N LEU I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE I 71 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 96 removed outlier: 4.050A pdb=" N ALA I 95 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU I 96 " --> pdb=" O PHE I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 96' Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'I' and resid 139 through 145 removed outlier: 3.825A pdb=" N ARG I 143 " --> pdb=" O GLY I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 338 removed outlier: 3.832A pdb=" N HIS I 337 " --> pdb=" O SER I 333 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU I 338 " --> pdb=" O PHE I 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 333 through 338' Processing helix chain 'I' and resid 509 through 513 Processing helix chain 'I' and resid 579 through 587 removed outlier: 3.554A pdb=" N HIS I 586 " --> pdb=" O ALA I 582 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN I 587 " --> pdb=" O ALA I 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.596A pdb=" N ASP A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.325A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.727A pdb=" N SER B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.601A pdb=" N ARG B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 4.145A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 removed outlier: 4.004A pdb=" N ILE B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.636A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 253 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 277' Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.663A pdb=" N LEU B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 Processing helix chain 'E' and resid 8 through 28 removed outlier: 3.686A pdb=" N LEU E 28 " --> pdb=" O ILE E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.874A pdb=" N LYS E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.794A pdb=" N GLN E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 removed outlier: 4.173A pdb=" N LEU E 218 " --> pdb=" O ARG E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'E' and resid 235 through 239 removed outlier: 4.132A pdb=" N ALA E 239 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 315 removed outlier: 3.650A pdb=" N ASN E 315 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 323 removed outlier: 4.300A pdb=" N SER E 322 " --> pdb=" O ASN E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 108 through 115 Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 171 through 182 Processing helix chain 'F' and resid 235 through 239 Processing helix chain 'F' and resid 310 through 318 removed outlier: 4.103A pdb=" N TYR F 314 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'I' and resid 102 through 103 removed outlier: 6.962A pdb=" N LEU I 102 " --> pdb=" O ASP I 130 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU I 129 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'I' and resid 270 through 271 removed outlier: 7.157A pdb=" N LEU I 344 " --> pdb=" O ASP I 369 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU I 368 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER I 449 " --> pdb=" O LEU I 415 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU I 448 " --> pdb=" O ASP I 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 353 through 354 Processing sheet with id=AA6, first strand: chain 'I' and resid 540 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.279A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 431 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.783A pdb=" N CYS A 59 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.814A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.810A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.506A pdb=" N ALA A 107 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.676A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 225 through 229 removed outlier: 3.954A pdb=" N SER A 225 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AB6, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB7, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.453A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN A 377 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.821A pdb=" N PHE A 473 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 540 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 541 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 512 " --> pdb=" O TYR A 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AC2, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AC3, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.779A pdb=" N LEU B 387 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 371 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.347A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 407 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 183 through 189 removed outlier: 3.557A pdb=" N VAL B 185 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE B 146 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER B 187 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B 144 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 189 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE B 142 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG B 236 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE B 298 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 238 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA B 300 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 240 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 345 through 346 Processing sheet with id=AC7, first strand: chain 'E' and resid 165 through 170 removed outlier: 5.335A pdb=" N VAL F 347 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N ARG E 81 " --> pdb=" O PRO F 345 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N VAL F 347 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N TYR F 340 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N GLN F 349 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL F 338 " --> pdb=" O GLN F 349 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N SER F 351 " --> pdb=" O PRO F 336 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET F 353 " --> pdb=" O PRO F 334 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL F 355 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU F 332 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER F 357 " --> pdb=" O GLN F 330 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU F 284 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N TYR F 340 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE F 282 " --> pdb=" O TYR F 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 101 through 105 removed outlier: 6.775A pdb=" N GLN E 137 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU E 157 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 139 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN E 155 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU E 141 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 265 through 268 removed outlier: 3.643A pdb=" N PHE E 292 " --> pdb=" O ARG E 267 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 282 through 284 removed outlier: 7.374A pdb=" N ILE E 282 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR E 340 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 284 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER E 357 " --> pdb=" O GLN E 330 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU E 332 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL E 355 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET E 353 " --> pdb=" O PRO E 334 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N SER E 351 " --> pdb=" O PRO E 336 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N VAL E 338 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N GLN E 349 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N TYR E 340 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N VAL E 347 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N ARG F 81 " --> pdb=" O PRO E 345 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL E 347 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F 77 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 125 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU F 165 " --> pdb=" O ARG F 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 101 through 107 removed outlier: 5.634A pdb=" N GLY F 187 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN F 143 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR F 152 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 265 through 267 removed outlier: 3.597A pdb=" N LEU F 294 " --> pdb=" O CYS F 265 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 270 through 272 390 hydrogen bonds defined for protein. 1005 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: 5.35 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4755 1.33 - 1.45: 2600 1.45 - 1.57: 9131 1.57 - 1.69: 1 1.69 - 1.82: 118 Bond restraints: 16605 Sorted by residual: bond pdb=" CA ILE I 330 " pdb=" C ILE I 330 " ideal model delta sigma weight residual 1.525 1.555 -0.030 8.80e-03 1.29e+04 1.13e+01 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" CZ ARG I 278 " pdb=" NH2 ARG I 278 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" CZ ARG I 348 " pdb=" NH2 ARG I 348 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.53e+00 bond pdb=" CZ ARG I 352 " pdb=" NH2 ARG I 352 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.08e+00 ... (remaining 16600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 21667 1.61 - 3.21: 751 3.21 - 4.82: 117 4.82 - 6.42: 20 6.42 - 8.03: 8 Bond angle restraints: 22563 Sorted by residual: angle pdb=" N ASP B 251 " pdb=" CA ASP B 251 " pdb=" C ASP B 251 " ideal model delta sigma weight residual 113.18 108.19 4.99 1.21e+00 6.83e-01 1.70e+01 angle pdb=" C ILE I 330 " pdb=" CA ILE I 330 " pdb=" CB ILE I 330 " ideal model delta sigma weight residual 110.85 115.50 -4.65 1.15e+00 7.56e-01 1.64e+01 angle pdb=" N ASN I 349 " pdb=" CA ASN I 349 " pdb=" C ASN I 349 " ideal model delta sigma weight residual 113.16 117.96 -4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" CA ASN I 325 " pdb=" CB ASN I 325 " pdb=" CG ASN I 325 " ideal model delta sigma weight residual 112.60 108.74 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CB HIS I 372 " pdb=" CG HIS I 372 " pdb=" CD2 HIS I 372 " ideal model delta sigma weight residual 131.20 126.28 4.92 1.30e+00 5.92e-01 1.43e+01 ... (remaining 22558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 9595 21.13 - 42.27: 593 42.27 - 63.40: 57 63.40 - 84.54: 20 84.54 - 105.67: 10 Dihedral angle restraints: 10275 sinusoidal: 4184 harmonic: 6091 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 39.43 53.57 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS I 425 " pdb=" SG CYS I 425 " pdb=" SG CYS I 436 " pdb=" CB CYS I 436 " ideal model delta sinusoidal sigma weight residual 93.00 41.78 51.22 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA CYS B 224 " pdb=" CB CYS B 224 " pdb=" SG CYS B 224 " pdb=" SG CYS B 265 " ideal model delta sinusoidal sigma weight residual -73.00 2.43 -75.43 1 2.00e+01 2.50e-03 1.80e+01 ... (remaining 10272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2164 0.061 - 0.122: 391 0.122 - 0.183: 32 0.183 - 0.244: 5 0.244 - 0.305: 5 Chirality restraints: 2597 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 44 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ASN I 274 " pdb=" N ASN I 274 " pdb=" C ASN I 274 " pdb=" CB ASN I 274 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2 BMA C 3 " pdb=" C1 BMA C 3 " pdb=" C3 BMA C 3 " pdb=" O2 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.47 2.75 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2594 not shown) Planarity restraints: 2938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 575 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A 576 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 576 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 576 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 395 " 0.019 2.00e-02 2.50e+03 1.70e-02 7.21e+00 pdb=" CG TRP A 395 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 395 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 395 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 395 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 395 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 395 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 395 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 395 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 395 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 372 " -0.027 2.00e-02 2.50e+03 2.03e-02 6.17e+00 pdb=" CG HIS I 372 " 0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS I 372 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS I 372 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS I 372 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS I 372 " -0.015 2.00e-02 2.50e+03 ... (remaining 2935 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 69 2.45 - 3.06: 10198 3.06 - 3.67: 22983 3.67 - 4.29: 34317 4.29 - 4.90: 59149 Nonbonded interactions: 126716 Sorted by model distance: nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B 504 " model vdw 1.833 2.170 nonbonded pdb=" OG SER B 116 " pdb="MG MG B 504 " model vdw 1.855 2.170 nonbonded pdb=" OD2 ASP B 151 " pdb="CA CA B 503 " model vdw 2.173 2.510 nonbonded pdb=" OD1 ASN E 107 " pdb=" OG SER E 109 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR E 99 " pdb=" OG1 THR E 202 " model vdw 2.212 3.040 ... (remaining 126711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'E' and (resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD )) or resid 6 or (resid 7 and (name N \ or name CA or name C or name O or name CB )) or resid 8 through 60 or resid 73 t \ hrough 210 or resid 224 through 361)) selection = (chain 'F' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 60 or resid 73 through 132 or resid 134 through 240 or resi \ d 262 through 301 or resid 310 through 361)) } 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: 16.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.910 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.005 0.061 16642 Z= 0.241 Angle : 0.727 10.759 22654 Z= 0.405 Chirality : 0.049 0.305 2597 Planarity : 0.004 0.077 2930 Dihedral : 13.626 105.671 6287 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.18), residues: 2079 helix: -0.47 (0.33), residues: 245 sheet: -1.40 (0.21), residues: 558 loop : -1.23 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 395 HIS 0.005 0.001 HIS E 222 PHE 0.015 0.001 PHE A 427 TYR 0.032 0.002 TYR A 275 ARG 0.011 0.001 ARG E 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 8) link_NAG-ASN : angle 1.75295 ( 24) link_ALPHA1-6 : bond 0.00621 ( 1) link_ALPHA1-6 : angle 2.24276 ( 3) link_BETA1-4 : bond 0.01222 ( 6) link_BETA1-4 : angle 3.13883 ( 18) link_ALPHA1-2 : bond 0.00184 ( 1) link_ALPHA1-2 : angle 1.86742 ( 3) link_ALPHA1-3 : bond 0.01085 ( 1) link_ALPHA1-3 : angle 1.19531 ( 3) hydrogen bonds : bond 0.23454 ( 384) hydrogen bonds : angle 9.36173 ( 1005) SS BOND : bond 0.00298 ( 20) SS BOND : angle 1.15085 ( 40) covalent geometry : bond 0.00502 (16605) covalent geometry : angle 0.71848 (22563) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 2.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3162 time to fit residues: 60.8325 Evaluate side-chains 102 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 99 optimal weight: 0.0050 chunk 121 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.130772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104998 restraints weight = 29274.538| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.51 r_work: 0.3248 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16642 Z= 0.164 Angle : 0.604 11.221 22654 Z= 0.307 Chirality : 0.044 0.210 2597 Planarity : 0.004 0.048 2930 Dihedral : 7.478 85.732 2619 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.60 % Allowed : 6.73 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2079 helix: -0.43 (0.33), residues: 252 sheet: -1.33 (0.21), residues: 593 loop : -1.05 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 114 HIS 0.005 0.001 HIS B 280 PHE 0.013 0.001 PHE A 427 TYR 0.019 0.001 TYR F 142 ARG 0.006 0.000 ARG I 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 8) link_NAG-ASN : angle 1.59984 ( 24) link_ALPHA1-6 : bond 0.00805 ( 1) link_ALPHA1-6 : angle 2.88387 ( 3) link_BETA1-4 : bond 0.01483 ( 6) link_BETA1-4 : angle 3.09525 ( 18) link_ALPHA1-2 : bond 0.00475 ( 1) link_ALPHA1-2 : angle 1.38314 ( 3) link_ALPHA1-3 : bond 0.01500 ( 1) link_ALPHA1-3 : angle 2.27080 ( 3) hydrogen bonds : bond 0.05055 ( 384) hydrogen bonds : angle 6.79205 ( 1005) SS BOND : bond 0.00262 ( 20) SS BOND : angle 0.85803 ( 40) covalent geometry : bond 0.00390 (16605) covalent geometry : angle 0.59402 (22563) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.771 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 117 average time/residue: 0.2842 time to fit residues: 50.2243 Evaluate side-chains 109 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain F residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 39 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 152 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105243 restraints weight = 29199.574| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.48 r_work: 0.3249 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16642 Z= 0.158 Angle : 0.563 11.227 22654 Z= 0.285 Chirality : 0.044 0.189 2597 Planarity : 0.004 0.044 2930 Dihedral : 6.706 70.722 2619 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.01 % Allowed : 9.06 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.18), residues: 2079 helix: -0.36 (0.33), residues: 259 sheet: -1.19 (0.21), residues: 583 loop : -1.07 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 114 HIS 0.004 0.001 HIS B 280 PHE 0.014 0.001 PHE A 19 TYR 0.013 0.001 TYR F 142 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 8) link_NAG-ASN : angle 1.59336 ( 24) link_ALPHA1-6 : bond 0.00897 ( 1) link_ALPHA1-6 : angle 2.91412 ( 3) link_BETA1-4 : bond 0.01533 ( 6) link_BETA1-4 : angle 3.12658 ( 18) link_ALPHA1-2 : bond 0.00460 ( 1) link_ALPHA1-2 : angle 1.36844 ( 3) link_ALPHA1-3 : bond 0.01730 ( 1) link_ALPHA1-3 : angle 2.11294 ( 3) hydrogen bonds : bond 0.04493 ( 384) hydrogen bonds : angle 6.23016 ( 1005) SS BOND : bond 0.00234 ( 20) SS BOND : angle 0.71579 ( 40) covalent geometry : bond 0.00375 (16605) covalent geometry : angle 0.55227 (22563) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.820 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 116 average time/residue: 0.2899 time to fit residues: 51.1698 Evaluate side-chains 111 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 12 optimal weight: 8.9990 chunk 136 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 420 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.132029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105782 restraints weight = 29148.152| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.55 r_work: 0.3261 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16642 Z= 0.122 Angle : 0.531 10.669 22654 Z= 0.267 Chirality : 0.043 0.203 2597 Planarity : 0.003 0.042 2930 Dihedral : 6.120 69.442 2619 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.25 % Allowed : 10.55 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2079 helix: -0.03 (0.35), residues: 247 sheet: -1.10 (0.21), residues: 567 loop : -1.02 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.004 0.001 HIS E 100 PHE 0.011 0.001 PHE A 427 TYR 0.013 0.001 TYR F 142 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 8) link_NAG-ASN : angle 1.48682 ( 24) link_ALPHA1-6 : bond 0.00946 ( 1) link_ALPHA1-6 : angle 2.67334 ( 3) link_BETA1-4 : bond 0.01444 ( 6) link_BETA1-4 : angle 3.00764 ( 18) link_ALPHA1-2 : bond 0.00381 ( 1) link_ALPHA1-2 : angle 1.30016 ( 3) link_ALPHA1-3 : bond 0.01689 ( 1) link_ALPHA1-3 : angle 2.33677 ( 3) hydrogen bonds : bond 0.03798 ( 384) hydrogen bonds : angle 5.94837 ( 1005) SS BOND : bond 0.00219 ( 20) SS BOND : angle 0.76739 ( 40) covalent geometry : bond 0.00290 (16605) covalent geometry : angle 0.51979 (22563) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 2.057 Fit side-chains revert: symmetry clash REVERT: B 192 ILE cc_start: 0.8170 (mm) cc_final: 0.7966 (mm) outliers start: 21 outliers final: 13 residues processed: 124 average time/residue: 0.2923 time to fit residues: 55.3821 Evaluate side-chains 113 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 174 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.131392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105205 restraints weight = 29485.348| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.58 r_work: 0.3248 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16642 Z= 0.151 Angle : 0.556 10.820 22654 Z= 0.280 Chirality : 0.044 0.276 2597 Planarity : 0.004 0.041 2930 Dihedral : 5.893 66.100 2619 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.03 % Allowed : 10.85 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2079 helix: -0.05 (0.35), residues: 247 sheet: -1.09 (0.21), residues: 567 loop : -1.03 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.004 0.001 HIS I 181 PHE 0.015 0.001 PHE A 19 TYR 0.013 0.001 TYR F 142 ARG 0.002 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 8) link_NAG-ASN : angle 1.54482 ( 24) link_ALPHA1-6 : bond 0.00939 ( 1) link_ALPHA1-6 : angle 2.64254 ( 3) link_BETA1-4 : bond 0.01416 ( 6) link_BETA1-4 : angle 3.06001 ( 18) link_ALPHA1-2 : bond 0.00577 ( 1) link_ALPHA1-2 : angle 1.34668 ( 3) link_ALPHA1-3 : bond 0.01792 ( 1) link_ALPHA1-3 : angle 2.30555 ( 3) hydrogen bonds : bond 0.03992 ( 384) hydrogen bonds : angle 5.88742 ( 1005) SS BOND : bond 0.00264 ( 20) SS BOND : angle 1.39471 ( 40) covalent geometry : bond 0.00365 (16605) covalent geometry : angle 0.54344 (22563) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: I 212 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8930 (mm) REVERT: F 49 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8343 (tp) outliers start: 34 outliers final: 25 residues processed: 129 average time/residue: 0.2778 time to fit residues: 55.5226 Evaluate side-chains 125 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 204 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.131442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105398 restraints weight = 29217.663| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.57 r_work: 0.3256 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16642 Z= 0.132 Angle : 0.540 10.606 22654 Z= 0.271 Chirality : 0.043 0.260 2597 Planarity : 0.003 0.040 2930 Dihedral : 5.595 64.831 2619 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.97 % Allowed : 11.32 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.18), residues: 2079 helix: -0.01 (0.35), residues: 246 sheet: -1.08 (0.21), residues: 563 loop : -0.98 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.005 0.001 HIS E 100 PHE 0.013 0.001 PHE A 19 TYR 0.013 0.001 TYR F 142 ARG 0.003 0.000 ARG F 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 8) link_NAG-ASN : angle 1.47322 ( 24) link_ALPHA1-6 : bond 0.00939 ( 1) link_ALPHA1-6 : angle 2.58744 ( 3) link_BETA1-4 : bond 0.01378 ( 6) link_BETA1-4 : angle 3.01601 ( 18) link_ALPHA1-2 : bond 0.00505 ( 1) link_ALPHA1-2 : angle 1.32141 ( 3) link_ALPHA1-3 : bond 0.01774 ( 1) link_ALPHA1-3 : angle 2.37512 ( 3) hydrogen bonds : bond 0.03696 ( 384) hydrogen bonds : angle 5.78958 ( 1005) SS BOND : bond 0.00208 ( 20) SS BOND : angle 1.63382 ( 40) covalent geometry : bond 0.00318 (16605) covalent geometry : angle 0.52586 (22563) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: I 212 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8852 (mm) REVERT: A 261 MET cc_start: 0.9167 (tpp) cc_final: 0.8936 (tpp) REVERT: F 49 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8335 (tp) REVERT: F 311 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8452 (mp) outliers start: 33 outliers final: 24 residues processed: 130 average time/residue: 0.2730 time to fit residues: 54.4394 Evaluate side-chains 125 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 179 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.0670 chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 167 optimal weight: 5.9990 chunk 99 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.133818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108121 restraints weight = 29423.028| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.54 r_work: 0.3282 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16642 Z= 0.100 Angle : 0.514 10.268 22654 Z= 0.259 Chirality : 0.042 0.266 2597 Planarity : 0.003 0.041 2930 Dihedral : 5.246 65.695 2619 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.61 % Allowed : 12.16 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2079 helix: 0.04 (0.35), residues: 246 sheet: -0.97 (0.21), residues: 568 loop : -0.93 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 580 HIS 0.003 0.001 HIS I 181 PHE 0.010 0.001 PHE A 427 TYR 0.013 0.001 TYR F 142 ARG 0.006 0.000 ARG F 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 8) link_NAG-ASN : angle 1.39541 ( 24) link_ALPHA1-6 : bond 0.00960 ( 1) link_ALPHA1-6 : angle 2.44625 ( 3) link_BETA1-4 : bond 0.01384 ( 6) link_BETA1-4 : angle 2.93555 ( 18) link_ALPHA1-2 : bond 0.00565 ( 1) link_ALPHA1-2 : angle 1.40950 ( 3) link_ALPHA1-3 : bond 0.01675 ( 1) link_ALPHA1-3 : angle 2.35781 ( 3) hydrogen bonds : bond 0.03393 ( 384) hydrogen bonds : angle 5.64275 ( 1005) SS BOND : bond 0.00143 ( 20) SS BOND : angle 1.43537 ( 40) covalent geometry : bond 0.00233 (16605) covalent geometry : angle 0.50056 (22563) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.898 Fit side-chains revert: symmetry clash REVERT: I 212 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8826 (mm) REVERT: I 568 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7624 (mp) REVERT: A 261 MET cc_start: 0.9184 (tpp) cc_final: 0.8980 (tpp) REVERT: A 395 TRP cc_start: 0.7640 (m100) cc_final: 0.7202 (m100) REVERT: F 49 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8310 (tp) outliers start: 27 outliers final: 22 residues processed: 131 average time/residue: 0.2614 time to fit residues: 53.1678 Evaluate side-chains 124 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 90 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103875 restraints weight = 29071.090| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.43 r_work: 0.3228 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16642 Z= 0.219 Angle : 0.621 11.190 22654 Z= 0.313 Chirality : 0.046 0.286 2597 Planarity : 0.004 0.041 2930 Dihedral : 5.600 59.564 2619 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.21 % Allowed : 11.62 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2079 helix: -0.19 (0.34), residues: 253 sheet: -1.17 (0.21), residues: 557 loop : -1.04 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 114 HIS 0.006 0.001 HIS B 180 PHE 0.021 0.002 PHE A 19 TYR 0.018 0.002 TYR A 275 ARG 0.004 0.000 ARG F 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 8) link_NAG-ASN : angle 1.64225 ( 24) link_ALPHA1-6 : bond 0.00869 ( 1) link_ALPHA1-6 : angle 2.50494 ( 3) link_BETA1-4 : bond 0.01430 ( 6) link_BETA1-4 : angle 3.18050 ( 18) link_ALPHA1-2 : bond 0.00612 ( 1) link_ALPHA1-2 : angle 1.21311 ( 3) link_ALPHA1-3 : bond 0.02000 ( 1) link_ALPHA1-3 : angle 2.36516 ( 3) hydrogen bonds : bond 0.04286 ( 384) hydrogen bonds : angle 5.88859 ( 1005) SS BOND : bond 0.00302 ( 20) SS BOND : angle 1.70320 ( 40) covalent geometry : bond 0.00530 (16605) covalent geometry : angle 0.60731 (22563) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: I 196 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8266 (mt) REVERT: I 212 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8968 (mm) REVERT: A 261 MET cc_start: 0.9147 (tpp) cc_final: 0.8924 (tpp) REVERT: F 49 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8392 (tp) REVERT: F 311 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8486 (mp) outliers start: 37 outliers final: 25 residues processed: 134 average time/residue: 0.2705 time to fit residues: 55.9532 Evaluate side-chains 131 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 373 ASN Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 110 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 131 optimal weight: 0.4980 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 0.3980 chunk 173 optimal weight: 8.9990 chunk 146 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.132702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106452 restraints weight = 29187.276| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.53 r_work: 0.3280 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16642 Z= 0.096 Angle : 0.514 10.198 22654 Z= 0.258 Chirality : 0.042 0.246 2597 Planarity : 0.003 0.042 2930 Dihedral : 5.074 63.222 2619 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.25 % Allowed : 12.75 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2079 helix: 0.15 (0.36), residues: 240 sheet: -0.89 (0.21), residues: 569 loop : -0.95 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 150 HIS 0.004 0.001 HIS E 100 PHE 0.009 0.001 PHE A 427 TYR 0.012 0.001 TYR F 142 ARG 0.003 0.000 ARG B 378 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 8) link_NAG-ASN : angle 1.35883 ( 24) link_ALPHA1-6 : bond 0.00891 ( 1) link_ALPHA1-6 : angle 2.32707 ( 3) link_BETA1-4 : bond 0.01346 ( 6) link_BETA1-4 : angle 2.94413 ( 18) link_ALPHA1-2 : bond 0.00443 ( 1) link_ALPHA1-2 : angle 1.41770 ( 3) link_ALPHA1-3 : bond 0.02016 ( 1) link_ALPHA1-3 : angle 2.54424 ( 3) hydrogen bonds : bond 0.03290 ( 384) hydrogen bonds : angle 5.60851 ( 1005) SS BOND : bond 0.00173 ( 20) SS BOND : angle 1.10736 ( 40) covalent geometry : bond 0.00218 (16605) covalent geometry : angle 0.50191 (22563) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.845 Fit side-chains REVERT: I 196 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8127 (mt) REVERT: I 212 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8813 (mm) REVERT: F 49 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8298 (tp) REVERT: F 311 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8443 (mp) outliers start: 21 outliers final: 12 residues processed: 125 average time/residue: 0.2997 time to fit residues: 57.2927 Evaluate side-chains 118 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 79 optimal weight: 4.9990 chunk 111 optimal weight: 0.0870 chunk 174 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105615 restraints weight = 29252.787| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.51 r_work: 0.3265 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16642 Z= 0.125 Angle : 0.533 10.488 22654 Z= 0.267 Chirality : 0.043 0.234 2597 Planarity : 0.003 0.041 2930 Dihedral : 5.024 62.653 2619 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.07 % Allowed : 13.17 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.18), residues: 2079 helix: -0.02 (0.35), residues: 252 sheet: -0.96 (0.21), residues: 575 loop : -0.93 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 395 HIS 0.004 0.001 HIS E 100 PHE 0.013 0.001 PHE A 19 TYR 0.012 0.001 TYR F 142 ARG 0.003 0.000 ARG B 378 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 8) link_NAG-ASN : angle 1.43712 ( 24) link_ALPHA1-6 : bond 0.00899 ( 1) link_ALPHA1-6 : angle 2.22320 ( 3) link_BETA1-4 : bond 0.01327 ( 6) link_BETA1-4 : angle 3.00607 ( 18) link_ALPHA1-2 : bond 0.00569 ( 1) link_ALPHA1-2 : angle 1.30168 ( 3) link_ALPHA1-3 : bond 0.01720 ( 1) link_ALPHA1-3 : angle 2.26171 ( 3) hydrogen bonds : bond 0.03512 ( 384) hydrogen bonds : angle 5.59255 ( 1005) SS BOND : bond 0.00168 ( 20) SS BOND : angle 1.20465 ( 40) covalent geometry : bond 0.00299 (16605) covalent geometry : angle 0.52126 (22563) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.820 Fit side-chains REVERT: I 196 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8192 (mt) REVERT: I 212 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8850 (mm) REVERT: F 49 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8318 (tp) REVERT: F 151 ARG cc_start: 0.7729 (tmm-80) cc_final: 0.7437 (tmm-80) REVERT: F 311 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8456 (mp) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 0.2816 time to fit residues: 51.6469 Evaluate side-chains 116 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 79 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.131102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.105312 restraints weight = 29432.752| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.47 r_work: 0.3239 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16642 Z= 0.185 Angle : 0.591 10.973 22654 Z= 0.296 Chirality : 0.045 0.257 2597 Planarity : 0.004 0.041 2930 Dihedral : 5.261 59.913 2619 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.55 % Allowed : 12.81 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2079 helix: -0.16 (0.34), residues: 259 sheet: -1.07 (0.21), residues: 565 loop : -0.99 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 395 HIS 0.005 0.001 HIS B 180 PHE 0.020 0.001 PHE A 19 TYR 0.015 0.002 TYR E 145 ARG 0.003 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 8) link_NAG-ASN : angle 1.57225 ( 24) link_ALPHA1-6 : bond 0.00856 ( 1) link_ALPHA1-6 : angle 2.28204 ( 3) link_BETA1-4 : bond 0.01348 ( 6) link_BETA1-4 : angle 3.12733 ( 18) link_ALPHA1-2 : bond 0.00574 ( 1) link_ALPHA1-2 : angle 1.24742 ( 3) link_ALPHA1-3 : bond 0.01907 ( 1) link_ALPHA1-3 : angle 2.27732 ( 3) hydrogen bonds : bond 0.03970 ( 384) hydrogen bonds : angle 5.73888 ( 1005) SS BOND : bond 0.00245 ( 20) SS BOND : angle 1.43102 ( 40) covalent geometry : bond 0.00450 (16605) covalent geometry : angle 0.57859 (22563) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9542.90 seconds wall clock time: 165 minutes 40.83 seconds (9940.83 seconds total)