Starting phenix.real_space_refine on Fri Jul 25 17:15:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b00_11952/07_2025/7b00_11952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b00_11952/07_2025/7b00_11952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2025/7b00_11952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2025/7b00_11952.map" model { file = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2025/7b00_11952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2025/7b00_11952.cif" } resolution = 3.98 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4833 2.51 5 N 1179 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7389 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3542 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain: "B" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "C" 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: "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: "E" 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 85 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.92, per 1000 atoms: 0.80 Number of scatterers: 7389 At special positions: 0 Unit cell: (81.6, 77.35, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1350 8.00 N 1179 7.00 C 4833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS B 109 " 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN B 405 " " NAG D 1 " - " ASN B 264 " " NAG E 1 " - " ASN B 280 " " NAG F 1 " - " ASN B 323 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 793.4 milliseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 48.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 removed outlier: 4.818A pdb=" N ASN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.967A pdb=" N GLU A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 68' Processing helix chain 'A' and resid 77 through 100 removed outlier: 4.190A pdb=" N GLY A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.851A pdb=" N LYS A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.643A pdb=" N GLY A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.761A pdb=" N SER A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 178 removed outlier: 4.500A pdb=" N ILE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.510A pdb=" N ARG A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 186' Processing helix chain 'A' and resid 187 through 190 Processing helix chain 'A' and resid 191 through 212 removed outlier: 3.993A pdb=" N ILE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 4.498A pdb=" N VAL A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.728A pdb=" N VAL A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.870A pdb=" N THR A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.754A pdb=" N ALA A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.972A pdb=" N ALA A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.586A pdb=" N LEU A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.828A pdb=" N ASN A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 412 removed outlier: 3.759A pdb=" N VAL A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 403 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.808A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.699A pdb=" N LEU A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.738A pdb=" N TRP A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 444' Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.288A pdb=" N MET A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 476 through 491 removed outlier: 3.688A pdb=" N ILE A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 removed outlier: 3.687A pdb=" N VAL B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 106 removed outlier: 3.535A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.534A pdb=" N HIS B 119 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 120 " --> pdb=" O TRP B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 120' Processing helix chain 'B' and resid 128 through 134 removed outlier: 3.729A pdb=" N GLN B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.898A pdb=" N LYS B 144 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 145 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.570A pdb=" N SER B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.503A pdb=" N THR B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 228' Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.701A pdb=" N GLU B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 252 removed outlier: 3.580A pdb=" N LEU B 252 " --> pdb=" O ILE B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.502A pdb=" N TRP B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.716A pdb=" N ILE B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.993A pdb=" N THR B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 357 removed outlier: 3.520A pdb=" N GLN B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.565A pdb=" N MET B 406 " --> pdb=" O SER B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 418 through 427 removed outlier: 3.918A pdb=" N ASP B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.596A pdb=" N HIS B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 160 removed outlier: 6.277A pdb=" N LEU B 205 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ARG B 247 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 275 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 300 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA B 277 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.542A pdb=" N LYS B 165 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 442 removed outlier: 3.632A pdb=" N VAL B 465 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 519 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 520 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER B 497 " --> pdb=" O GLY B 520 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 522 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 493 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 508 " --> pdb=" O ALA B 492 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2204 1.34 - 1.46: 1444 1.46 - 1.57: 3894 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 7583 Sorted by residual: bond pdb=" C56 AJP A 601 " pdb=" C57 AJP A 601 " ideal model delta sigma weight residual 1.522 1.558 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" C65 AJP A 601 " pdb=" O64 AJP A 601 " ideal model delta sigma weight residual 1.373 1.408 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C57 AJP A 601 " pdb=" O64 AJP A 601 " ideal model delta sigma weight residual 1.414 1.443 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C3 NAG F 1 " pdb=" O3 NAG F 1 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 7578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 9953 2.20 - 4.41: 321 4.41 - 6.61: 50 6.61 - 8.81: 23 8.81 - 11.01: 3 Bond angle restraints: 10350 Sorted by residual: angle pdb=" N ARG B 433 " pdb=" CA ARG B 433 " pdb=" C ARG B 433 " ideal model delta sigma weight residual 114.56 108.83 5.73 1.27e+00 6.20e-01 2.04e+01 angle pdb=" C PRO A 364 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 120.33 123.54 -3.21 8.00e-01 1.56e+00 1.61e+01 angle pdb=" CA ILE A 365 " pdb=" C ILE A 365 " pdb=" N PRO A 366 " ideal model delta sigma weight residual 120.83 123.17 -2.34 6.10e-01 2.69e+00 1.47e+01 angle pdb=" C ASP A 230 " pdb=" N ILE A 231 " pdb=" CA ILE A 231 " ideal model delta sigma weight residual 121.97 128.74 -6.77 1.80e+00 3.09e-01 1.41e+01 angle pdb=" C SER A 444 " pdb=" N GLU A 445 " pdb=" CA GLU A 445 " ideal model delta sigma weight residual 121.80 130.57 -8.77 2.44e+00 1.68e-01 1.29e+01 ... (remaining 10345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 4376 24.70 - 49.39: 281 49.39 - 74.09: 21 74.09 - 98.79: 3 98.79 - 123.48: 17 Dihedral angle restraints: 4698 sinusoidal: 2050 harmonic: 2648 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS B 109 " pdb=" CB CYS B 109 " ideal model delta sinusoidal sigma weight residual -86.00 -39.60 -46.40 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CA LEU A 350 " pdb=" C LEU A 350 " pdb=" N PRO A 351 " pdb=" CA PRO A 351 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA THR A 133 " pdb=" C THR A 133 " pdb=" N ASN A 134 " pdb=" CA ASN A 134 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 4695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 1231 0.331 - 0.662: 2 0.662 - 0.992: 0 0.992 - 1.323: 0 1.323 - 1.654: 1 Chirality restraints: 1234 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 323 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.04e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.41e+01 ... (remaining 1231 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.343 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG F 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.272 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" C7 NAG F 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.383 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.224 2.00e-02 2.50e+03 1.91e-01 4.55e+02 pdb=" C7 NAG D 2 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.313 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.173 2.00e-02 2.50e+03 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 32 2.45 - 3.06: 4159 3.06 - 3.68: 11042 3.68 - 4.29: 15290 4.29 - 4.90: 24995 Nonbonded interactions: 55518 Sorted by model distance: nonbonded pdb=" O3 NAG D 1 " pdb=" O6 NAG D 1 " model vdw 1.838 3.040 nonbonded pdb=" O ILE A 138 " pdb=" OG1 THR A 326 " model vdw 2.241 3.040 nonbonded pdb=" O GLY A 332 " pdb=" OG1 THR A 336 " model vdw 2.272 3.040 nonbonded pdb=" O SER B 305 " pdb=" OG SER B 305 " model vdw 2.286 3.040 nonbonded pdb=" O SER B 302 " pdb=" OG SER B 302 " model vdw 2.298 3.040 ... (remaining 55513 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.010 0.668 7593 Z= 0.809 Angle : 1.025 14.113 10376 Z= 0.506 Chirality : 0.076 1.654 1234 Planarity : 0.014 0.297 1265 Dihedral : 17.032 123.481 2999 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.39 % Allowed : 12.24 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.20 (0.17), residues: 922 helix: -4.76 (0.09), residues: 417 sheet: -1.62 (0.66), residues: 52 loop : -3.77 (0.21), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 469 HIS 0.007 0.001 HIS A 358 PHE 0.022 0.002 PHE A 226 TYR 0.022 0.002 TYR A 93 ARG 0.004 0.001 ARG A 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 4) link_NAG-ASN : angle 9.94061 ( 12) link_BETA1-4 : bond 0.00098 ( 4) link_BETA1-4 : angle 0.31424 ( 12) hydrogen bonds : bond 0.34471 ( 215) hydrogen bonds : angle 11.56254 ( 627) SS BOND : bond 0.00107 ( 1) SS BOND : angle 1.40937 ( 2) covalent geometry : bond 0.00565 ( 7583) covalent geometry : angle 0.96811 (10350) Misc. bond : bond 0.66841 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.8369 (pt) cc_final: 0.8114 (mm) REVERT: A 184 THR cc_start: 0.8873 (t) cc_final: 0.8474 (m) REVERT: A 211 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7677 (ttpp) REVERT: A 264 ASN cc_start: 0.7982 (m-40) cc_final: 0.7700 (m-40) REVERT: A 284 ASN cc_start: 0.8556 (m-40) cc_final: 0.7769 (t0) REVERT: B 146 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7238 (mmt90) REVERT: B 187 GLU cc_start: 0.7815 (pm20) cc_final: 0.7584 (pm20) REVERT: B 432 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7429 (tp30) outliers start: 3 outliers final: 1 residues processed: 162 average time/residue: 0.1954 time to fit residues: 42.7170 Evaluate side-chains 121 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** 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 = 0.3792 r_free = 0.3792 target = 0.155741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122316 restraints weight = 10296.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121865 restraints weight = 14849.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122836 restraints weight = 14592.265| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7593 Z= 0.157 Angle : 0.775 13.230 10376 Z= 0.366 Chirality : 0.045 0.382 1234 Planarity : 0.005 0.048 1265 Dihedral : 13.186 103.068 1375 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.71 % Allowed : 17.40 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.21), residues: 922 helix: -3.34 (0.17), residues: 425 sheet: -1.43 (0.68), residues: 52 loop : -3.34 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 358 PHE 0.024 0.002 PHE A 155 TYR 0.014 0.001 TYR B 303 ARG 0.003 0.000 ARG B 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 4) link_NAG-ASN : angle 6.78726 ( 12) link_BETA1-4 : bond 0.00869 ( 4) link_BETA1-4 : angle 2.58002 ( 12) hydrogen bonds : bond 0.06244 ( 215) hydrogen bonds : angle 6.44646 ( 627) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.79433 ( 2) covalent geometry : bond 0.00350 ( 7583) covalent geometry : angle 0.73496 (10350) Misc. bond : bond 0.00470 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASN cc_start: 0.8544 (m-40) cc_final: 0.7986 (t0) REVERT: A 314 MET cc_start: 0.5731 (tpt) cc_final: 0.5335 (tpt) REVERT: B 336 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7870 (pt0) outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 0.1841 time to fit residues: 34.9122 Evaluate side-chains 127 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 6 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 381 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124641 restraints weight = 10355.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122669 restraints weight = 14344.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124150 restraints weight = 14108.521| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7593 Z= 0.113 Angle : 0.707 12.329 10376 Z= 0.326 Chirality : 0.042 0.294 1234 Planarity : 0.004 0.043 1265 Dihedral : 11.254 101.027 1375 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.25 % Allowed : 18.56 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.24), residues: 922 helix: -2.46 (0.21), residues: 424 sheet: -1.62 (0.57), residues: 70 loop : -3.09 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 117 HIS 0.003 0.001 HIS B 518 PHE 0.025 0.002 PHE A 433 TYR 0.011 0.001 TYR B 303 ARG 0.006 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 4) link_NAG-ASN : angle 6.63703 ( 12) link_BETA1-4 : bond 0.00683 ( 4) link_BETA1-4 : angle 2.34821 ( 12) hydrogen bonds : bond 0.04190 ( 215) hydrogen bonds : angle 5.41469 ( 627) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.58109 ( 2) covalent geometry : bond 0.00251 ( 7583) covalent geometry : angle 0.66633 (10350) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8692 (mm) cc_final: 0.8242 (mt) REVERT: A 284 ASN cc_start: 0.8369 (m-40) cc_final: 0.7873 (t0) REVERT: B 146 ARG cc_start: 0.7548 (mmt180) cc_final: 0.6842 (mmt90) REVERT: B 347 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6317 (pp30) outliers start: 33 outliers final: 25 residues processed: 148 average time/residue: 0.1669 time to fit residues: 34.4307 Evaluate side-chains 138 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 78 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** 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 = 0.3809 r_free = 0.3809 target = 0.157371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123260 restraints weight = 10404.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121873 restraints weight = 16877.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123098 restraints weight = 16002.890| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7593 Z= 0.136 Angle : 0.696 11.457 10376 Z= 0.323 Chirality : 0.043 0.309 1234 Planarity : 0.004 0.041 1265 Dihedral : 10.600 98.664 1375 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.77 % Allowed : 19.97 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.25), residues: 922 helix: -2.12 (0.22), residues: 433 sheet: -1.38 (0.61), residues: 69 loop : -2.95 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 262 HIS 0.003 0.001 HIS B 455 PHE 0.031 0.002 PHE A 155 TYR 0.010 0.001 TYR A 109 ARG 0.004 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 4) link_NAG-ASN : angle 6.41033 ( 12) link_BETA1-4 : bond 0.00694 ( 4) link_BETA1-4 : angle 2.36077 ( 12) hydrogen bonds : bond 0.03783 ( 215) hydrogen bonds : angle 5.25858 ( 627) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.71421 ( 2) covalent geometry : bond 0.00318 ( 7583) covalent geometry : angle 0.65697 (10350) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8788 (mm) cc_final: 0.8253 (mt) REVERT: A 284 ASN cc_start: 0.8534 (m-40) cc_final: 0.8033 (t0) REVERT: A 471 HIS cc_start: 0.3640 (OUTLIER) cc_final: 0.2312 (m-70) REVERT: B 146 ARG cc_start: 0.7541 (mmt180) cc_final: 0.7339 (mmt180) REVERT: B 262 TRP cc_start: 0.8187 (m-90) cc_final: 0.7928 (m-90) REVERT: B 347 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6387 (pp30) outliers start: 37 outliers final: 27 residues processed: 147 average time/residue: 0.1921 time to fit residues: 40.1852 Evaluate side-chains 144 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 90 optimal weight: 0.0050 chunk 0 optimal weight: 3.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** 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 = 0.3824 r_free = 0.3824 target = 0.159008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124837 restraints weight = 10221.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123113 restraints weight = 14576.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124385 restraints weight = 14619.032| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7593 Z= 0.112 Angle : 0.663 10.647 10376 Z= 0.307 Chirality : 0.042 0.300 1234 Planarity : 0.004 0.040 1265 Dihedral : 10.049 93.996 1375 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.77 % Allowed : 19.85 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.26), residues: 922 helix: -1.80 (0.23), residues: 433 sheet: -1.23 (0.63), residues: 69 loop : -2.82 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 262 HIS 0.002 0.001 HIS B 518 PHE 0.027 0.001 PHE A 155 TYR 0.009 0.001 TYR A 109 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 4) link_NAG-ASN : angle 5.59484 ( 12) link_BETA1-4 : bond 0.00734 ( 4) link_BETA1-4 : angle 2.44180 ( 12) hydrogen bonds : bond 0.03296 ( 215) hydrogen bonds : angle 4.98229 ( 627) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.51717 ( 2) covalent geometry : bond 0.00255 ( 7583) covalent geometry : angle 0.63039 (10350) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8781 (mm) cc_final: 0.8260 (mt) REVERT: A 184 THR cc_start: 0.8795 (t) cc_final: 0.8442 (m) REVERT: A 284 ASN cc_start: 0.8513 (m-40) cc_final: 0.8007 (t0) REVERT: A 471 HIS cc_start: 0.3719 (OUTLIER) cc_final: 0.2290 (m-70) REVERT: B 262 TRP cc_start: 0.8270 (m-10) cc_final: 0.8001 (m-90) REVERT: B 347 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6475 (pp30) outliers start: 37 outliers final: 28 residues processed: 147 average time/residue: 0.1908 time to fit residues: 38.6217 Evaluate side-chains 141 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 0.0270 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.156560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122290 restraints weight = 10433.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120912 restraints weight = 16418.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122362 restraints weight = 17541.562| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7593 Z= 0.169 Angle : 0.713 10.511 10376 Z= 0.332 Chirality : 0.045 0.299 1234 Planarity : 0.004 0.041 1265 Dihedral : 10.101 91.596 1375 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.51 % Allowed : 20.62 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.26), residues: 922 helix: -1.65 (0.24), residues: 443 sheet: -1.31 (0.62), residues: 69 loop : -2.77 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 262 HIS 0.004 0.001 HIS B 455 PHE 0.023 0.002 PHE A 155 TYR 0.011 0.001 TYR A 109 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 4) link_NAG-ASN : angle 5.46589 ( 12) link_BETA1-4 : bond 0.00789 ( 4) link_BETA1-4 : angle 2.42115 ( 12) hydrogen bonds : bond 0.03593 ( 215) hydrogen bonds : angle 5.12693 ( 627) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.83070 ( 2) covalent geometry : bond 0.00402 ( 7583) covalent geometry : angle 0.68455 (10350) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.4701 (pm20) REVERT: A 284 ASN cc_start: 0.8521 (m-40) cc_final: 0.8173 (t0) REVERT: A 471 HIS cc_start: 0.3773 (OUTLIER) cc_final: 0.2393 (m-70) REVERT: B 262 TRP cc_start: 0.8225 (m-10) cc_final: 0.7978 (m-90) REVERT: B 347 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6459 (pp30) outliers start: 35 outliers final: 29 residues processed: 133 average time/residue: 0.1635 time to fit residues: 30.7710 Evaluate side-chains 137 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 0.0030 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** 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 = 0.3809 r_free = 0.3809 target = 0.157675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122838 restraints weight = 10307.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121884 restraints weight = 16240.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123101 restraints weight = 16142.262| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7593 Z= 0.133 Angle : 0.694 10.214 10376 Z= 0.319 Chirality : 0.044 0.290 1234 Planarity : 0.004 0.039 1265 Dihedral : 9.750 87.501 1375 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.15 % Allowed : 21.26 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.27), residues: 922 helix: -1.43 (0.24), residues: 440 sheet: -1.38 (0.61), residues: 70 loop : -2.71 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 262 HIS 0.003 0.001 HIS B 455 PHE 0.022 0.002 PHE A 155 TYR 0.010 0.001 TYR A 109 ARG 0.002 0.000 ARG B 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 4) link_NAG-ASN : angle 5.19991 ( 12) link_BETA1-4 : bond 0.00837 ( 4) link_BETA1-4 : angle 2.61236 ( 12) hydrogen bonds : bond 0.03326 ( 215) hydrogen bonds : angle 4.97614 ( 627) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.72321 ( 2) covalent geometry : bond 0.00314 ( 7583) covalent geometry : angle 0.66570 (10350) Misc. bond : bond 0.00206 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 THR cc_start: 0.8863 (t) cc_final: 0.8492 (m) REVERT: A 284 ASN cc_start: 0.8520 (m-40) cc_final: 0.8028 (t0) REVERT: A 464 PHE cc_start: 0.5736 (OUTLIER) cc_final: 0.5499 (m-10) REVERT: A 471 HIS cc_start: 0.3831 (OUTLIER) cc_final: 0.2465 (m-70) REVERT: B 262 TRP cc_start: 0.8335 (m-10) cc_final: 0.8088 (m-90) REVERT: B 299 LEU cc_start: 0.8888 (tp) cc_final: 0.8683 (mt) REVERT: B 347 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6498 (pp30) outliers start: 40 outliers final: 29 residues processed: 134 average time/residue: 0.1700 time to fit residues: 32.2523 Evaluate side-chains 136 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 57 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 86 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.156475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121718 restraints weight = 10404.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120823 restraints weight = 15867.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121986 restraints weight = 16437.050| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7593 Z= 0.162 Angle : 0.715 11.656 10376 Z= 0.332 Chirality : 0.045 0.288 1234 Planarity : 0.004 0.040 1265 Dihedral : 9.586 84.157 1375 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.38 % Allowed : 22.68 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.27), residues: 922 helix: -1.33 (0.25), residues: 444 sheet: -1.40 (0.61), residues: 70 loop : -2.67 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 262 HIS 0.003 0.001 HIS B 455 PHE 0.035 0.002 PHE A 155 TYR 0.024 0.001 TYR B 303 ARG 0.003 0.000 ARG B 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 4) link_NAG-ASN : angle 5.14834 ( 12) link_BETA1-4 : bond 0.00975 ( 4) link_BETA1-4 : angle 2.65135 ( 12) hydrogen bonds : bond 0.03449 ( 215) hydrogen bonds : angle 5.00970 ( 627) SS BOND : bond 0.00513 ( 1) SS BOND : angle 1.16543 ( 2) covalent geometry : bond 0.00386 ( 7583) covalent geometry : angle 0.68759 (10350) Misc. bond : bond 0.00330 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.6957 (mm) REVERT: A 284 ASN cc_start: 0.8579 (m-40) cc_final: 0.8123 (t0) REVERT: A 471 HIS cc_start: 0.3935 (OUTLIER) cc_final: 0.2571 (m-70) REVERT: B 262 TRP cc_start: 0.8373 (m-10) cc_final: 0.8125 (m-90) REVERT: B 347 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6511 (pp30) outliers start: 34 outliers final: 27 residues processed: 130 average time/residue: 0.1764 time to fit residues: 31.7925 Evaluate side-chains 134 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 19 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 56 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 58 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** 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 = 0.3819 r_free = 0.3819 target = 0.158492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124155 restraints weight = 10296.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122773 restraints weight = 16636.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123895 restraints weight = 15110.293| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7593 Z= 0.126 Angle : 0.764 24.318 10376 Z= 0.341 Chirality : 0.046 0.487 1234 Planarity : 0.004 0.042 1265 Dihedral : 9.355 81.174 1375 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.51 % Allowed : 23.07 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.81 (0.27), residues: 922 helix: -1.23 (0.25), residues: 445 sheet: -1.29 (0.62), residues: 70 loop : -2.68 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 262 HIS 0.002 0.001 HIS A 349 PHE 0.035 0.002 PHE A 155 TYR 0.016 0.001 TYR A 109 ARG 0.003 0.000 ARG B 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 4) link_NAG-ASN : angle 4.98157 ( 12) link_BETA1-4 : bond 0.00908 ( 4) link_BETA1-4 : angle 2.75342 ( 12) hydrogen bonds : bond 0.03162 ( 215) hydrogen bonds : angle 4.82891 ( 627) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.77852 ( 2) covalent geometry : bond 0.00291 ( 7583) covalent geometry : angle 0.73944 (10350) Misc. bond : bond 0.01398 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6798 (mm) REVERT: A 124 TRP cc_start: 0.8389 (OUTLIER) cc_final: 0.7613 (t60) REVERT: A 184 THR cc_start: 0.8924 (t) cc_final: 0.8551 (m) REVERT: A 284 ASN cc_start: 0.8477 (m-40) cc_final: 0.8015 (t0) REVERT: A 445 GLU cc_start: 0.8162 (pm20) cc_final: 0.7952 (pm20) REVERT: A 471 HIS cc_start: 0.3896 (OUTLIER) cc_final: 0.2601 (m-70) REVERT: B 258 PHE cc_start: 0.6417 (m-80) cc_final: 0.5993 (m-80) REVERT: B 262 TRP cc_start: 0.8363 (m-10) cc_final: 0.8109 (m-90) REVERT: B 347 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6508 (pp30) outliers start: 35 outliers final: 29 residues processed: 135 average time/residue: 0.1724 time to fit residues: 32.3333 Evaluate side-chains 134 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 0.0370 chunk 34 optimal weight: 0.3980 chunk 28 optimal weight: 0.0770 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.0470 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** 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 = 0.3849 r_free = 0.3849 target = 0.161335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125288 restraints weight = 10327.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123798 restraints weight = 12588.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125553 restraints weight = 12395.288| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7593 Z= 0.109 Angle : 0.740 20.695 10376 Z= 0.332 Chirality : 0.046 0.480 1234 Planarity : 0.004 0.036 1265 Dihedral : 8.935 74.787 1375 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.61 % Allowed : 23.97 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.52 (0.27), residues: 922 helix: -0.96 (0.25), residues: 440 sheet: -1.12 (0.65), residues: 60 loop : -2.53 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 262 HIS 0.002 0.001 HIS A 349 PHE 0.035 0.001 PHE A 155 TYR 0.027 0.001 TYR B 303 ARG 0.003 0.000 ARG B 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 4) link_NAG-ASN : angle 4.77986 ( 12) link_BETA1-4 : bond 0.00993 ( 4) link_BETA1-4 : angle 2.85253 ( 12) hydrogen bonds : bond 0.02878 ( 215) hydrogen bonds : angle 4.64181 ( 627) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.58491 ( 2) covalent geometry : bond 0.00239 ( 7583) covalent geometry : angle 0.71658 (10350) Misc. bond : bond 0.01266 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.6776 (mm) REVERT: A 49 ILE cc_start: 0.8493 (mm) cc_final: 0.8094 (mt) REVERT: A 184 THR cc_start: 0.8826 (t) cc_final: 0.8522 (m) REVERT: A 228 GLU cc_start: 0.5230 (OUTLIER) cc_final: 0.4601 (pm20) REVERT: A 284 ASN cc_start: 0.8480 (m-40) cc_final: 0.8045 (t0) REVERT: A 421 LYS cc_start: 0.7320 (tptt) cc_final: 0.6102 (mtmm) REVERT: A 471 HIS cc_start: 0.3781 (OUTLIER) cc_final: 0.2693 (m-70) REVERT: B 258 PHE cc_start: 0.6470 (m-80) cc_final: 0.6022 (m-80) REVERT: B 262 TRP cc_start: 0.8376 (m-10) cc_final: 0.8122 (m-90) REVERT: B 347 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6540 (pp30) outliers start: 28 outliers final: 22 residues processed: 136 average time/residue: 0.1675 time to fit residues: 31.9624 Evaluate side-chains 135 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 88 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** 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 = 0.3861 r_free = 0.3861 target = 0.162450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127889 restraints weight = 10099.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125737 restraints weight = 16565.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127978 restraints weight = 16363.589| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 7593 Z= 0.111 Angle : 0.744 19.524 10376 Z= 0.335 Chirality : 0.046 0.439 1234 Planarity : 0.004 0.037 1265 Dihedral : 8.665 69.890 1375 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.48 % Allowed : 24.36 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.44 (0.27), residues: 922 helix: -0.89 (0.25), residues: 446 sheet: -1.00 (0.66), residues: 60 loop : -2.54 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 124 HIS 0.002 0.001 HIS A 349 PHE 0.035 0.001 PHE A 155 TYR 0.016 0.001 TYR A 109 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 4) link_NAG-ASN : angle 4.69649 ( 12) link_BETA1-4 : bond 0.00965 ( 4) link_BETA1-4 : angle 2.85982 ( 12) hydrogen bonds : bond 0.02841 ( 215) hydrogen bonds : angle 4.58947 ( 627) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.53277 ( 2) covalent geometry : bond 0.00243 ( 7583) covalent geometry : angle 0.72106 (10350) Misc. bond : bond 0.01115 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.68 seconds wall clock time: 44 minutes 29.54 seconds (2669.54 seconds total)