Starting phenix.real_space_refine on Fri Aug 22 20:55:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b00_11952/08_2025/7b00_11952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b00_11952/08_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_11952/08_2025/7b00_11952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b00_11952/08_2025/7b00_11952.map" model { file = "/net/cci-nas-00/data/ceres_data/7b00_11952/08_2025/7b00_11952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b00_11952/08_2025/7b00_11952.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.94, per 1000 atoms: 0.26 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: 0.69 Conformation dependent library (CDL) restraints added in 579.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.24 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: 0.98 Time building geometry restraints manager: 0.92 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: 5.540 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- 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 : 6.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.001 ARG A 122 TYR 0.022 0.002 TYR A 93 PHE 0.022 0.002 PHE A 226 TRP 0.018 0.002 TRP A 469 HIS 0.007 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 7583) covalent geometry : angle 0.96811 (10350) SS BOND : bond 0.00107 ( 1) SS BOND : angle 1.40937 ( 2) hydrogen bonds : bond 0.34471 ( 215) hydrogen bonds : angle 11.56254 ( 627) Misc. bond : bond 0.66841 ( 1) link_BETA1-4 : bond 0.00098 ( 4) link_BETA1-4 : angle 0.31424 ( 12) link_NAG-ASN : bond 0.00527 ( 4) link_NAG-ASN : angle 9.94061 ( 12) *********************** 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 : 0.262 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: 0.8473 (m) REVERT: A 211 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7678 (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: 0.0860 time to fit residues: 18.9081 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 : 0.274 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.155780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121913 restraints weight = 10397.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120989 restraints weight = 14961.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122147 restraints weight = 15538.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122800 restraints weight = 10479.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122943 restraints weight = 10102.738| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1688 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= 0.156 Angle : 0.776 13.124 10376 Z= 0.367 Chirality : 0.046 0.391 1234 Planarity : 0.005 0.048 1265 Dihedral : 13.140 102.624 1375 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.71 % Allowed : 17.53 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.000 ARG B 338 TYR 0.013 0.001 TYR B 303 PHE 0.025 0.002 PHE A 155 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7583) covalent geometry : angle 0.73744 (10350) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.80293 ( 2) hydrogen bonds : bond 0.06181 ( 215) hydrogen bonds : angle 6.43829 ( 627) Misc. bond : bond 0.00948 ( 1) link_BETA1-4 : bond 0.00980 ( 4) link_BETA1-4 : angle 2.63550 ( 12) link_NAG-ASN : bond 0.00613 ( 4) link_NAG-ASN : angle 6.69302 ( 12) *********************** 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 147 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASN cc_start: 0.8523 (m-40) cc_final: 0.7968 (t0) REVERT: A 314 MET cc_start: 0.5725 (tpt) cc_final: 0.5331 (tpt) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 0.0843 time to fit residues: 16.2069 Evaluate side-chains 125 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 14 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121955 restraints weight = 10454.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123435 restraints weight = 15646.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124365 restraints weight = 14511.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124398 restraints weight = 9697.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124588 restraints weight = 10836.222| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2184 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= 0.170 Angle : 0.747 11.893 10376 Z= 0.349 Chirality : 0.044 0.293 1234 Planarity : 0.004 0.046 1265 Dihedral : 11.653 103.383 1375 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.03 % Allowed : 18.94 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.16 (0.24), residues: 922 helix: -2.56 (0.21), residues: 435 sheet: -1.72 (0.58), residues: 69 loop : -3.13 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 105 TYR 0.012 0.001 TYR A 109 PHE 0.024 0.002 PHE A 155 TRP 0.010 0.001 TRP A 124 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7583) covalent geometry : angle 0.70710 (10350) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.90383 ( 2) hydrogen bonds : bond 0.04678 ( 215) hydrogen bonds : angle 5.68554 ( 627) Misc. bond : bond 0.00021 ( 1) link_BETA1-4 : bond 0.00725 ( 4) link_BETA1-4 : angle 2.26872 ( 12) link_NAG-ASN : bond 0.00607 ( 4) link_NAG-ASN : angle 6.77333 ( 12) *********************** 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: 39 poor density : 119 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.0703 (OUTLIER) cc_final: 0.0487 (tt) REVERT: A 284 ASN cc_start: 0.8485 (m-40) cc_final: 0.8026 (t0) REVERT: A 471 HIS cc_start: 0.3715 (OUTLIER) cc_final: 0.2415 (m-70) REVERT: B 146 ARG cc_start: 0.7493 (mmt180) cc_final: 0.7263 (mmt180) REVERT: B 347 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6379 (pp30) outliers start: 39 outliers final: 25 residues processed: 148 average time/residue: 0.0756 time to fit residues: 15.5632 Evaluate side-chains 140 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 163 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 258 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 377 LEU 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 460 VAL Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain A residue 482 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 0.0030 chunk 0 optimal weight: 1.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 GLN ** 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 = 0.3815 r_free = 0.3815 target = 0.158002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123553 restraints weight = 10414.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122138 restraints weight = 16196.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123676 restraints weight = 14975.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123897 restraints weight = 10966.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124207 restraints weight = 11173.064| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7593 Z= 0.115 Angle : 0.689 11.387 10376 Z= 0.320 Chirality : 0.042 0.301 1234 Planarity : 0.004 0.044 1265 Dihedral : 10.648 99.294 1375 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.99 % Allowed : 20.88 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.25), residues: 922 helix: -2.14 (0.22), residues: 434 sheet: -1.48 (0.61), residues: 69 loop : -3.00 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 105 TYR 0.014 0.001 TYR B 149 PHE 0.025 0.001 PHE A 155 TRP 0.040 0.001 TRP B 262 HIS 0.002 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7583) covalent geometry : angle 0.64930 (10350) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.44680 ( 2) hydrogen bonds : bond 0.03663 ( 215) hydrogen bonds : angle 5.26437 ( 627) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00780 ( 4) link_BETA1-4 : angle 2.53848 ( 12) link_NAG-ASN : bond 0.00687 ( 4) link_NAG-ASN : angle 6.36603 ( 12) *********************** 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 152 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8736 (mm) cc_final: 0.8277 (mt) REVERT: A 184 THR cc_start: 0.8884 (t) cc_final: 0.8519 (m) REVERT: A 284 ASN cc_start: 0.8485 (m-40) cc_final: 0.7947 (t0) REVERT: A 471 HIS cc_start: 0.3738 (OUTLIER) cc_final: 0.2448 (m-70) REVERT: B 146 ARG cc_start: 0.7561 (mmt180) cc_final: 0.7357 (mmt180) REVERT: B 262 TRP cc_start: 0.8249 (m-90) cc_final: 0.7961 (m-90) REVERT: B 347 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6435 (pp30) outliers start: 31 outliers final: 21 residues processed: 144 average time/residue: 0.0727 time to fit residues: 14.8042 Evaluate side-chains 133 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 473 LEU 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 27 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.158392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124651 restraints weight = 10325.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122480 restraints weight = 15290.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123850 restraints weight = 14950.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124375 restraints weight = 10515.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124464 restraints weight = 10642.885| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7593 Z= 0.114 Angle : 0.685 10.761 10376 Z= 0.315 Chirality : 0.042 0.300 1234 Planarity : 0.004 0.042 1265 Dihedral : 10.331 95.525 1375 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.90 % Allowed : 20.62 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.25), residues: 922 helix: -1.84 (0.23), residues: 434 sheet: -1.34 (0.62), residues: 69 loop : -2.87 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.011 0.001 TYR B 149 PHE 0.034 0.002 PHE A 155 TRP 0.021 0.001 TRP B 262 HIS 0.002 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7583) covalent geometry : angle 0.65202 (10350) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.52095 ( 2) hydrogen bonds : bond 0.03316 ( 215) hydrogen bonds : angle 5.02974 ( 627) Misc. bond : bond 0.00215 ( 1) link_BETA1-4 : bond 0.00720 ( 4) link_BETA1-4 : angle 2.45085 ( 12) link_NAG-ASN : bond 0.00597 ( 4) link_NAG-ASN : angle 5.70166 ( 12) *********************** 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 155 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8747 (mm) cc_final: 0.8217 (mt) REVERT: A 184 THR cc_start: 0.8844 (t) cc_final: 0.8499 (m) REVERT: A 284 ASN cc_start: 0.8526 (m-40) cc_final: 0.8004 (t0) REVERT: A 471 HIS cc_start: 0.3756 (OUTLIER) cc_final: 0.2451 (m-70) REVERT: B 262 TRP cc_start: 0.8303 (m-10) cc_final: 0.7976 (m-90) REVERT: B 347 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6487 (pp30) outliers start: 38 outliers final: 29 residues processed: 144 average time/residue: 0.0731 time to fit residues: 14.9747 Evaluate side-chains 136 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 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 A residue 482 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3805 r_free = 0.3805 target = 0.157253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127616 restraints weight = 10445.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128039 restraints weight = 15064.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126727 restraints weight = 13345.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126277 restraints weight = 11849.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126626 restraints weight = 11156.672| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2721 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= 0.145 Angle : 0.694 10.504 10376 Z= 0.322 Chirality : 0.044 0.293 1234 Planarity : 0.004 0.043 1265 Dihedral : 10.085 92.124 1375 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.38 % Allowed : 22.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.26), residues: 922 helix: -1.65 (0.24), residues: 437 sheet: -1.32 (0.62), residues: 69 loop : -2.83 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.010 0.001 TYR B 149 PHE 0.028 0.002 PHE A 155 TRP 0.014 0.001 TRP B 262 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7583) covalent geometry : angle 0.66403 (10350) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.73476 ( 2) hydrogen bonds : bond 0.03420 ( 215) hydrogen bonds : angle 5.04753 ( 627) Misc. bond : bond 0.00431 ( 1) link_BETA1-4 : bond 0.00741 ( 4) link_BETA1-4 : angle 2.46877 ( 12) link_NAG-ASN : bond 0.00539 ( 4) link_NAG-ASN : angle 5.43965 ( 12) *********************** 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: 34 poor density : 110 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 THR cc_start: 0.8818 (t) cc_final: 0.8434 (m) REVERT: A 284 ASN cc_start: 0.8536 (m-40) cc_final: 0.8074 (t0) REVERT: A 445 GLU cc_start: 0.8109 (pm20) cc_final: 0.7887 (pm20) REVERT: A 471 HIS cc_start: 0.3707 (OUTLIER) cc_final: 0.2367 (m-70) REVERT: B 299 LEU cc_start: 0.8906 (tp) cc_final: 0.8664 (mt) REVERT: B 347 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6429 (pp30) outliers start: 34 outliers final: 29 residues processed: 132 average time/residue: 0.0708 time to fit residues: 13.2201 Evaluate side-chains 136 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 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 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 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 9 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.159084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125146 restraints weight = 10475.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124509 restraints weight = 16481.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126166 restraints weight = 15923.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126251 restraints weight = 10410.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126693 restraints weight = 10827.535| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7593 Z= 0.113 Angle : 0.669 10.247 10376 Z= 0.309 Chirality : 0.043 0.289 1234 Planarity : 0.004 0.039 1265 Dihedral : 9.676 87.894 1375 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.90 % Allowed : 21.39 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.26), residues: 922 helix: -1.48 (0.24), residues: 436 sheet: -1.37 (0.62), residues: 70 loop : -2.69 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.009 0.001 TYR B 149 PHE 0.028 0.001 PHE A 155 TRP 0.054 0.001 TRP B 262 HIS 0.002 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7583) covalent geometry : angle 0.63973 (10350) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.50586 ( 2) hydrogen bonds : bond 0.03143 ( 215) hydrogen bonds : angle 4.87454 ( 627) Misc. bond : bond 0.00289 ( 1) link_BETA1-4 : bond 0.00912 ( 4) link_BETA1-4 : angle 2.64484 ( 12) link_NAG-ASN : bond 0.00529 ( 4) link_NAG-ASN : angle 5.15562 ( 12) *********************** 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 147 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 THR cc_start: 0.8842 (t) cc_final: 0.8503 (m) REVERT: A 284 ASN cc_start: 0.8422 (m-40) cc_final: 0.7971 (t0) REVERT: A 464 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5600 (m-10) REVERT: A 471 HIS cc_start: 0.3718 (OUTLIER) cc_final: 0.2364 (m-70) REVERT: B 262 TRP cc_start: 0.8082 (m-90) cc_final: 0.7730 (m-90) REVERT: B 347 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6484 (pp30) outliers start: 38 outliers final: 27 residues processed: 136 average time/residue: 0.0627 time to fit residues: 12.1624 Evaluate side-chains 136 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 164 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 231 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 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 464 PHE 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 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 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 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 78 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.159123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123454 restraints weight = 10352.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122468 restraints weight = 14281.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123907 restraints weight = 14460.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123858 restraints weight = 9579.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124327 restraints weight = 9809.594| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7593 Z= 0.130 Angle : 0.729 17.887 10376 Z= 0.330 Chirality : 0.046 0.404 1234 Planarity : 0.004 0.039 1265 Dihedral : 9.570 85.000 1375 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.51 % Allowed : 22.42 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.97 (0.27), residues: 922 helix: -1.38 (0.24), residues: 444 sheet: -1.34 (0.62), residues: 70 loop : -2.75 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.023 0.001 TYR B 303 PHE 0.026 0.002 PHE A 433 TRP 0.042 0.001 TRP B 262 HIS 0.002 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7583) covalent geometry : angle 0.70347 (10350) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.62595 ( 2) hydrogen bonds : bond 0.03168 ( 215) hydrogen bonds : angle 4.85050 ( 627) Misc. bond : bond 0.01166 ( 1) link_BETA1-4 : bond 0.00914 ( 4) link_BETA1-4 : angle 2.61783 ( 12) link_NAG-ASN : bond 0.00491 ( 4) link_NAG-ASN : angle 5.05557 ( 12) *********************** 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 140 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6922 (mm) REVERT: A 184 THR cc_start: 0.8880 (t) cc_final: 0.8529 (m) REVERT: A 284 ASN cc_start: 0.8479 (m-40) cc_final: 0.8063 (t0) REVERT: A 464 PHE cc_start: 0.5810 (OUTLIER) cc_final: 0.5561 (m-10) REVERT: A 471 HIS cc_start: 0.3750 (OUTLIER) cc_final: 0.2383 (m-70) REVERT: B 262 TRP cc_start: 0.8202 (m-90) cc_final: 0.7862 (m-90) REVERT: B 347 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6506 (pp30) outliers start: 35 outliers final: 25 residues processed: 131 average time/residue: 0.0742 time to fit residues: 13.8935 Evaluate side-chains 132 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 164 LEU Chi-restraints excluded: chain A residue 173 THR 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 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 448 VAL 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 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 45 optimal weight: 0.0070 chunk 30 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.160062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127563 restraints weight = 10187.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123231 restraints weight = 11308.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123441 restraints weight = 12259.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123947 restraints weight = 11054.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124494 restraints weight = 9403.029| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7593 Z= 0.115 Angle : 0.702 14.684 10376 Z= 0.319 Chirality : 0.046 0.441 1234 Planarity : 0.003 0.037 1265 Dihedral : 9.296 81.006 1375 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.27), residues: 922 helix: -1.21 (0.25), residues: 441 sheet: -1.21 (0.63), residues: 70 loop : -2.69 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.011 0.001 TYR A 109 PHE 0.028 0.001 PHE A 433 TRP 0.037 0.001 TRP B 262 HIS 0.002 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7583) covalent geometry : angle 0.67654 (10350) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.79613 ( 2) hydrogen bonds : bond 0.03011 ( 215) hydrogen bonds : angle 4.71272 ( 627) Misc. bond : bond 0.01141 ( 1) link_BETA1-4 : bond 0.00900 ( 4) link_BETA1-4 : angle 2.71402 ( 12) link_NAG-ASN : bond 0.00510 ( 4) link_NAG-ASN : angle 4.91398 ( 12) *********************** 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 142 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6872 (mm) REVERT: A 124 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.7326 (t60) REVERT: A 184 THR cc_start: 0.8805 (t) cc_final: 0.8470 (m) REVERT: A 284 ASN cc_start: 0.8459 (m-40) cc_final: 0.8141 (t0) REVERT: A 464 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5571 (m-10) REVERT: A 469 TRP cc_start: 0.4379 (p-90) cc_final: 0.3656 (p-90) REVERT: A 471 HIS cc_start: 0.3809 (OUTLIER) cc_final: 0.2490 (m-70) REVERT: B 262 TRP cc_start: 0.8326 (m-90) cc_final: 0.7983 (m-90) REVERT: B 347 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6496 (pp30) outliers start: 34 outliers final: 24 residues processed: 134 average time/residue: 0.0715 time to fit residues: 13.8541 Evaluate side-chains 133 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 124 TRP Chi-restraints excluded: chain A residue 125 ILE 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 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL 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 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 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 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 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 = 0.3820 r_free = 0.3820 target = 0.158542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123963 restraints weight = 10278.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122795 restraints weight = 16603.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124365 restraints weight = 16146.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124571 restraints weight = 10689.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124776 restraints weight = 10234.484| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7593 Z= 0.142 Angle : 0.704 9.850 10376 Z= 0.325 Chirality : 0.046 0.332 1234 Planarity : 0.004 0.037 1265 Dihedral : 9.159 78.025 1375 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.87 % Allowed : 23.07 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.27), residues: 922 helix: -1.10 (0.25), residues: 444 sheet: -1.24 (0.62), residues: 70 loop : -2.71 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.024 0.001 TYR B 303 PHE 0.036 0.002 PHE A 155 TRP 0.035 0.001 TRP B 262 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7583) covalent geometry : angle 0.67840 (10350) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.99089 ( 2) hydrogen bonds : bond 0.03187 ( 215) hydrogen bonds : angle 4.79711 ( 627) Misc. bond : bond 0.00719 ( 1) link_BETA1-4 : bond 0.00890 ( 4) link_BETA1-4 : angle 2.73222 ( 12) link_NAG-ASN : bond 0.00458 ( 4) link_NAG-ASN : angle 4.91107 ( 12) ********************** 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 134 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7429 (t60) REVERT: A 184 THR cc_start: 0.8890 (t) cc_final: 0.8544 (m) REVERT: A 284 ASN cc_start: 0.8518 (m-40) cc_final: 0.8070 (t0) REVERT: A 464 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.5567 (m-10) REVERT: A 471 HIS cc_start: 0.3735 (OUTLIER) cc_final: 0.2360 (m-70) REVERT: B 262 TRP cc_start: 0.8272 (m-90) cc_final: 0.8007 (m-90) REVERT: B 347 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6502 (pp30) outliers start: 30 outliers final: 25 residues processed: 126 average time/residue: 0.0655 time to fit residues: 12.1887 Evaluate side-chains 132 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 124 TRP Chi-restraints excluded: chain A residue 125 ILE 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 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 0.0980 chunk 72 optimal weight: 0.0370 chunk 45 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 90 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.0000 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.1200 ------------------------------------------------------------------------------- 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 = 0.162512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128716 restraints weight = 10197.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126786 restraints weight = 15264.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128059 restraints weight = 14996.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128665 restraints weight = 10331.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128994 restraints weight = 10162.682| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7593 Z= 0.106 Angle : 0.681 9.668 10376 Z= 0.312 Chirality : 0.043 0.272 1234 Planarity : 0.003 0.034 1265 Dihedral : 8.700 72.567 1375 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.27), residues: 922 helix: -0.86 (0.25), residues: 441 sheet: -1.11 (0.66), residues: 60 loop : -2.56 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.016 0.001 TYR A 109 PHE 0.039 0.001 PHE A 155 TRP 0.035 0.001 TRP B 262 HIS 0.001 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7583) covalent geometry : angle 0.65603 (10350) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.48438 ( 2) hydrogen bonds : bond 0.02786 ( 215) hydrogen bonds : angle 4.56183 ( 627) Misc. bond : bond 0.00583 ( 1) link_BETA1-4 : bond 0.01003 ( 4) link_BETA1-4 : angle 2.84316 ( 12) link_NAG-ASN : bond 0.00556 ( 4) link_NAG-ASN : angle 4.70676 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.33 seconds wall clock time: 21 minutes 41.56 seconds (1301.56 seconds total)