Starting phenix.real_space_refine on Sun Jul 27 05:55:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fl7_50532/07_2025/9fl7_50532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fl7_50532/07_2025/9fl7_50532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fl7_50532/07_2025/9fl7_50532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fl7_50532/07_2025/9fl7_50532.map" model { file = "/net/cci-nas-00/data/ceres_data/9fl7_50532/07_2025/9fl7_50532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fl7_50532/07_2025/9fl7_50532.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.153 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 34 5.16 5 C 5666 2.51 5 N 1584 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8969 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3499 Classifications: {'peptide': 453} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3442 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 21, 'TRANS': 423} Chain breaks: 1 Chain: "D" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1834 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 219} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.82, per 1000 atoms: 0.65 Number of scatterers: 8969 At special positions: 0 Unit cell: (86.7, 122.4, 119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 8 15.00 O 1677 8.00 N 1584 7.00 C 5666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 92 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 17 sheets defined 34.7% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 140 through 154 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.545A pdb=" N ILE A 220 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 removed outlier: 3.626A pdb=" N ASP A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.709A pdb=" N LYS A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 309 through 327 removed outlier: 3.511A pdb=" N SER A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 4.256A pdb=" N GLU A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.136A pdb=" N LYS A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.779A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.754A pdb=" N ALA A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.762A pdb=" N VAL A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.525A pdb=" N PHE B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 4.322A pdb=" N SER B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.527A pdb=" N ARG B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 286 through 300 removed outlier: 4.336A pdb=" N ARG B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 327 removed outlier: 3.584A pdb=" N SER B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 removed outlier: 4.319A pdb=" N GLU B 354 " --> pdb=" O ASN B 350 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 357 " --> pdb=" O MET B 353 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 471 removed outlier: 3.774A pdb=" N THR B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 595 removed outlier: 3.669A pdb=" N ALA B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'D' and resid 27 through 40 Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.680A pdb=" N GLY D 57 " --> pdb=" O MET D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 70 Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.554A pdb=" N THR D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.705A pdb=" N GLU D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 196 through 203 removed outlier: 3.644A pdb=" N TYR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 230 removed outlier: 3.728A pdb=" N LYS D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 229 removed outlier: 3.761A pdb=" N ALA A 226 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 163 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 430 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 435 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLN A 428 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 264 removed outlier: 3.737A pdb=" N GLU A 401 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.522A pdb=" N THR A 282 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 396 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER A 302 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N VAL A 395 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR A 304 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 303 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 333 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 375 removed outlier: 3.552A pdb=" N ILE A 381 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 389 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 442 through 443 Processing sheet with id=AA7, first strand: chain 'A' and resid 481 through 486 removed outlier: 3.884A pdb=" N VAL A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR A 567 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 565 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU A 578 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY A 563 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS A 562 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET D 237 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY A 506 " --> pdb=" O MET D 237 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE D 239 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHE A 508 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 228 removed outlier: 3.740A pdb=" N VAL B 159 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL B 132 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU B 160 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N PHE B 134 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL B 162 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 136 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N HIS B 131 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N LYS B 255 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 257 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 135 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 244 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 235 " --> pdb=" O LYS B 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 228 removed outlier: 3.740A pdb=" N VAL B 159 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL B 132 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU B 160 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N PHE B 134 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL B 162 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 136 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N HIS B 131 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N LYS B 255 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 257 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 135 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N TRP B 434 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS B 256 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AB2, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AB3, first strand: chain 'B' and resid 362 through 364 removed outlier: 6.366A pdb=" N VAL B 330 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N MET B 364 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN B 332 " --> pdb=" O MET B 364 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 303 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER B 302 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL B 395 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N THR B 304 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 369 through 375 removed outlier: 3.514A pdb=" N SER B 371 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 421 through 422 removed outlier: 7.081A pdb=" N PHE B 421 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TYR B 443 " --> pdb=" O PHE B 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 442 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 450 " --> pdb=" O PHE B 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 484 through 486 removed outlier: 3.747A pdb=" N VAL B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 576 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE B 576 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU B 578 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLY B 563 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 566 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 505 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.701A pdb=" N LEU D 98 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL D 19 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE D 128 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU D 21 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 143 through 144 305 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2957 1.34 - 1.47: 1985 1.47 - 1.59: 4140 1.59 - 1.72: 22 1.72 - 1.84: 58 Bond restraints: 9162 Sorted by residual: bond pdb=" O2A NAD B 701 " pdb=" PA NAD B 701 " ideal model delta sigma weight residual 1.491 1.610 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" O2A NAD A 701 " pdb=" PA NAD A 701 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" O2A FAD A 702 " pdb=" PA FAD A 702 " ideal model delta sigma weight residual 1.494 1.611 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" O2A FAD B 702 " pdb=" PA FAD B 702 " ideal model delta sigma weight residual 1.494 1.610 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O2P FAD B 702 " pdb=" P FAD B 702 " ideal model delta sigma weight residual 1.495 1.610 -0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 9157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.55: 12333 4.55 - 9.09: 62 9.09 - 13.64: 13 13.64 - 18.18: 8 18.18 - 22.73: 2 Bond angle restraints: 12418 Sorted by residual: angle pdb=" P FAD B 702 " pdb=" O3P FAD B 702 " pdb=" PA FAD B 702 " ideal model delta sigma weight residual 130.34 107.61 22.73 3.00e+00 1.11e-01 5.74e+01 angle pdb=" P FAD A 702 " pdb=" O3P FAD A 702 " pdb=" PA FAD A 702 " ideal model delta sigma weight residual 130.34 109.75 20.59 3.00e+00 1.11e-01 4.71e+01 angle pdb=" PA NAD A 701 " pdb=" O3 NAD A 701 " pdb=" PN NAD A 701 " ideal model delta sigma weight residual 126.50 108.82 17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" PA NAD B 701 " pdb=" O3 NAD B 701 " pdb=" PN NAD B 701 " ideal model delta sigma weight residual 126.50 109.29 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C5' FAD A 702 " pdb=" O5' FAD A 702 " pdb=" P FAD A 702 " ideal model delta sigma weight residual 121.27 106.17 15.10 3.00e+00 1.11e-01 2.53e+01 ... (remaining 12413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 5055 17.50 - 35.00: 431 35.00 - 52.50: 117 52.50 - 70.00: 24 70.00 - 87.49: 8 Dihedral angle restraints: 5635 sinusoidal: 2419 harmonic: 3216 Sorted by residual: dihedral pdb=" CB CYS D 42 " pdb=" SG CYS D 42 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual -86.00 -6.93 -79.07 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CA ASP B 600 " pdb=" CB ASP B 600 " pdb=" CG ASP B 600 " pdb=" OD1 ASP B 600 " ideal model delta sinusoidal sigma weight residual -30.00 -87.00 57.00 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB MET D 53 " pdb=" CG MET D 53 " pdb=" SD MET D 53 " pdb=" CE MET D 53 " ideal model delta sinusoidal sigma weight residual -180.00 -121.15 -58.85 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1102 0.056 - 0.112: 222 0.112 - 0.169: 30 0.169 - 0.225: 13 0.225 - 0.281: 7 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C1B NAD A 701 " pdb=" C2B NAD A 701 " pdb=" N9A NAD A 701 " pdb=" O4B NAD A 701 " both_signs ideal model delta sigma weight residual False 2.35 2.63 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C1B FAD A 702 " pdb=" C2B FAD A 702 " pdb=" N9A FAD A 702 " pdb=" O4B FAD A 702 " both_signs ideal model delta sigma weight residual False 2.35 2.61 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C4D NAD B 701 " pdb=" C3D NAD B 701 " pdb=" C5D NAD B 701 " pdb=" O4D NAD B 701 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1371 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 172 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO B 173 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 173 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 174 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 195 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO D 196 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " 0.019 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1253 2.76 - 3.29: 8905 3.29 - 3.83: 14900 3.83 - 4.36: 16464 4.36 - 4.90: 27936 Nonbonded interactions: 69458 Sorted by model distance: nonbonded pdb=" OD2 ASP D 112 " pdb=" OH TYR D 200 " model vdw 2.224 3.040 nonbonded pdb=" O3' FAD A 702 " pdb=" O5' FAD A 702 " model vdw 2.239 3.040 nonbonded pdb=" OG SER A 302 " pdb=" OE2 GLU A 329 " model vdw 2.248 3.040 nonbonded pdb=" O LEU D 64 " pdb=" OG1 THR D 67 " model vdw 2.271 3.040 nonbonded pdb=" NE ARG B 265 " pdb=" OE2 GLU B 401 " model vdw 2.278 3.120 ... (remaining 69453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 128 through 512 or resid 549 or resid 552 or resid 557 thr \ ough 611 or resid 701 through 702)) selection = (chain 'B' and (resid 128 through 514 or resid 557 through 611 or resid 701 thro \ ugh 702)) } 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.380 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 9163 Z= 0.296 Angle : 0.973 22.729 12420 Z= 0.429 Chirality : 0.052 0.281 1374 Planarity : 0.004 0.046 1582 Dihedral : 14.576 87.494 3570 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.43 % Allowed : 0.53 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1124 helix: 0.67 (0.30), residues: 328 sheet: -0.39 (0.36), residues: 220 loop : -0.68 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 434 HIS 0.002 0.001 HIS A 454 PHE 0.009 0.001 PHE D 227 TYR 0.006 0.001 TYR D 190 ARG 0.003 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.22016 ( 302) hydrogen bonds : angle 7.99983 ( 861) SS BOND : bond 0.00722 ( 1) SS BOND : angle 6.77128 ( 2) covalent geometry : bond 0.00535 ( 9162) covalent geometry : angle 0.96881 (12418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8357 (m-30) cc_final: 0.8032 (t0) REVERT: A 284 PHE cc_start: 0.8455 (t80) cc_final: 0.8024 (t80) REVERT: A 333 LEU cc_start: 0.9482 (pp) cc_final: 0.9054 (tt) REVERT: A 364 MET cc_start: 0.8269 (tpt) cc_final: 0.7886 (tpt) REVERT: A 456 ASP cc_start: 0.8487 (t0) cc_final: 0.8097 (t70) REVERT: A 486 LEU cc_start: 0.9368 (mt) cc_final: 0.8610 (tp) REVERT: A 492 TYR cc_start: 0.8865 (p90) cc_final: 0.8425 (p90) REVERT: A 585 MET cc_start: 0.8217 (tmm) cc_final: 0.8013 (tmm) REVERT: B 253 TYR cc_start: 0.8942 (p90) cc_final: 0.8680 (p90) REVERT: B 255 LYS cc_start: 0.9474 (mptt) cc_final: 0.9251 (mmmt) REVERT: B 340 MET cc_start: 0.8043 (mmt) cc_final: 0.7797 (mmt) REVERT: B 364 MET cc_start: 0.8788 (mpp) cc_final: 0.8385 (mpp) REVERT: B 481 MET cc_start: 0.8677 (ptt) cc_final: 0.8141 (ptp) REVERT: B 567 TYR cc_start: 0.7901 (m-80) cc_final: 0.7616 (m-80) REVERT: D 20 LEU cc_start: 0.8354 (tp) cc_final: 0.7924 (tp) REVERT: D 21 LEU cc_start: 0.8918 (mt) cc_final: 0.8533 (mt) outliers start: 4 outliers final: 2 residues processed: 159 average time/residue: 0.2284 time to fit residues: 49.3150 Evaluate side-chains 105 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.089552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.065793 restraints weight = 40125.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067793 restraints weight = 23946.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069178 restraints weight = 16743.391| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9163 Z= 0.181 Angle : 0.620 9.110 12420 Z= 0.316 Chirality : 0.045 0.199 1374 Planarity : 0.004 0.041 1582 Dihedral : 10.034 83.639 1431 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.32 % Allowed : 5.13 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1124 helix: 0.59 (0.29), residues: 335 sheet: -0.27 (0.37), residues: 187 loop : -0.81 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 579 HIS 0.004 0.001 HIS A 454 PHE 0.021 0.001 PHE B 508 TYR 0.024 0.002 TYR A 443 ARG 0.004 0.000 ARG A 450 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 302) hydrogen bonds : angle 6.35540 ( 861) SS BOND : bond 0.01014 ( 1) SS BOND : angle 4.09079 ( 2) covalent geometry : bond 0.00389 ( 9162) covalent geometry : angle 0.61786 (12418) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8336 (m-30) cc_final: 0.8056 (t0) REVERT: A 333 LEU cc_start: 0.9466 (pp) cc_final: 0.9076 (tt) REVERT: A 364 MET cc_start: 0.8051 (tpt) cc_final: 0.7745 (tpt) REVERT: A 456 ASP cc_start: 0.8210 (t0) cc_final: 0.7980 (t70) REVERT: A 492 TYR cc_start: 0.8580 (p90) cc_final: 0.8067 (p90) REVERT: A 585 MET cc_start: 0.8160 (tmm) cc_final: 0.7954 (tmm) REVERT: B 171 MET cc_start: 0.8468 (ttm) cc_final: 0.8204 (mtm) REVERT: B 253 TYR cc_start: 0.8899 (p90) cc_final: 0.8644 (p90) REVERT: B 340 MET cc_start: 0.8390 (mmt) cc_final: 0.7740 (mmt) REVERT: B 364 MET cc_start: 0.8766 (mpp) cc_final: 0.8464 (mpp) REVERT: B 481 MET cc_start: 0.8864 (ptt) cc_final: 0.8387 (ptp) REVERT: D 20 LEU cc_start: 0.8394 (tp) cc_final: 0.8028 (tt) REVERT: D 21 LEU cc_start: 0.8530 (mt) cc_final: 0.7975 (mt) REVERT: D 191 HIS cc_start: 0.9415 (m90) cc_final: 0.8918 (m90) REVERT: D 201 TYR cc_start: 0.9389 (m-10) cc_final: 0.9140 (m-10) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 0.2707 time to fit residues: 49.8968 Evaluate side-chains 87 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 85 optimal weight: 0.0670 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.089694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066599 restraints weight = 41224.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068595 restraints weight = 24532.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069934 restraints weight = 17166.879| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9163 Z= 0.124 Angle : 0.560 7.821 12420 Z= 0.285 Chirality : 0.045 0.140 1374 Planarity : 0.004 0.043 1582 Dihedral : 9.234 87.489 1431 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1124 helix: 0.43 (0.29), residues: 344 sheet: -0.53 (0.36), residues: 194 loop : -0.86 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 434 HIS 0.002 0.001 HIS A 457 PHE 0.021 0.001 PHE D 227 TYR 0.022 0.001 TYR A 347 ARG 0.004 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 302) hydrogen bonds : angle 5.90329 ( 861) SS BOND : bond 0.00690 ( 1) SS BOND : angle 2.71703 ( 2) covalent geometry : bond 0.00267 ( 9162) covalent geometry : angle 0.55914 (12418) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8326 (m-30) cc_final: 0.8085 (t0) REVERT: A 315 LEU cc_start: 0.9699 (mt) cc_final: 0.9477 (mt) REVERT: A 333 LEU cc_start: 0.9531 (pp) cc_final: 0.9146 (tt) REVERT: A 364 MET cc_start: 0.8038 (tpt) cc_final: 0.7689 (tpt) REVERT: A 456 ASP cc_start: 0.8180 (t0) cc_final: 0.7956 (t70) REVERT: A 486 LEU cc_start: 0.9449 (mm) cc_final: 0.8645 (tp) REVERT: A 492 TYR cc_start: 0.8472 (p90) cc_final: 0.8055 (p90) REVERT: B 340 MET cc_start: 0.8144 (mmt) cc_final: 0.7860 (mmt) REVERT: B 364 MET cc_start: 0.8735 (mpp) cc_final: 0.8361 (mpp) REVERT: B 481 MET cc_start: 0.8919 (ptt) cc_final: 0.8406 (ptp) REVERT: B 585 MET cc_start: 0.8505 (tpt) cc_final: 0.8288 (tpt) REVERT: D 20 LEU cc_start: 0.8377 (tp) cc_final: 0.7897 (tt) REVERT: D 21 LEU cc_start: 0.8446 (mt) cc_final: 0.7947 (mt) REVERT: D 191 HIS cc_start: 0.9439 (m90) cc_final: 0.8916 (m90) REVERT: D 201 TYR cc_start: 0.9257 (m-10) cc_final: 0.9019 (m-10) REVERT: D 234 ASP cc_start: 0.8240 (p0) cc_final: 0.8033 (p0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2902 time to fit residues: 50.5130 Evaluate side-chains 91 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.089839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066195 restraints weight = 39756.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068153 restraints weight = 23812.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069453 restraints weight = 16678.217| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9163 Z= 0.124 Angle : 0.552 6.717 12420 Z= 0.283 Chirality : 0.044 0.139 1374 Planarity : 0.004 0.041 1582 Dihedral : 8.793 87.612 1431 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1124 helix: 0.43 (0.30), residues: 341 sheet: -0.53 (0.36), residues: 193 loop : -0.86 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 434 HIS 0.005 0.001 HIS A 454 PHE 0.026 0.001 PHE D 227 TYR 0.023 0.001 TYR A 347 ARG 0.014 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 302) hydrogen bonds : angle 5.73889 ( 861) SS BOND : bond 0.00606 ( 1) SS BOND : angle 2.09203 ( 2) covalent geometry : bond 0.00270 ( 9162) covalent geometry : angle 0.55148 (12418) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8252 (m-30) cc_final: 0.8022 (t0) REVERT: A 333 LEU cc_start: 0.9507 (pp) cc_final: 0.9142 (tt) REVERT: A 364 MET cc_start: 0.8055 (tpt) cc_final: 0.7770 (tpt) REVERT: A 492 TYR cc_start: 0.8437 (p90) cc_final: 0.7990 (p90) REVERT: A 585 MET cc_start: 0.8305 (tmm) cc_final: 0.8046 (tmm) REVERT: B 340 MET cc_start: 0.8144 (mmt) cc_final: 0.7854 (mmt) REVERT: B 364 MET cc_start: 0.8724 (mpp) cc_final: 0.8378 (mpp) REVERT: B 456 ASP cc_start: 0.8687 (t0) cc_final: 0.7764 (t70) REVERT: B 481 MET cc_start: 0.8958 (ptt) cc_final: 0.8156 (pmm) REVERT: B 565 ILE cc_start: 0.9162 (mt) cc_final: 0.8937 (mm) REVERT: B 567 TYR cc_start: 0.7842 (m-10) cc_final: 0.7635 (m-80) REVERT: B 585 MET cc_start: 0.8539 (tpt) cc_final: 0.8304 (tpt) REVERT: D 20 LEU cc_start: 0.8467 (tp) cc_final: 0.8026 (tt) REVERT: D 21 LEU cc_start: 0.8592 (mt) cc_final: 0.7959 (mt) REVERT: D 35 LEU cc_start: 0.9056 (mt) cc_final: 0.8774 (mt) REVERT: D 191 HIS cc_start: 0.9425 (m90) cc_final: 0.8884 (m90) REVERT: D 201 TYR cc_start: 0.9083 (m-10) cc_final: 0.8880 (m-10) REVERT: D 220 PHE cc_start: 0.9018 (t80) cc_final: 0.8191 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2020 time to fit residues: 35.4309 Evaluate side-chains 88 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 0.0030 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 597 GLN D 31 GLN D 43 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.088990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065453 restraints weight = 40081.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067307 restraints weight = 23912.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068503 restraints weight = 16831.984| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9163 Z= 0.143 Angle : 0.567 11.426 12420 Z= 0.288 Chirality : 0.044 0.136 1374 Planarity : 0.004 0.034 1582 Dihedral : 8.506 87.080 1431 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1124 helix: 0.46 (0.29), residues: 341 sheet: -0.62 (0.36), residues: 200 loop : -0.83 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 483 HIS 0.007 0.001 HIS D 43 PHE 0.025 0.001 PHE A 482 TYR 0.011 0.001 TYR B 253 ARG 0.002 0.000 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 302) hydrogen bonds : angle 5.49226 ( 861) SS BOND : bond 0.00803 ( 1) SS BOND : angle 4.95975 ( 2) covalent geometry : bond 0.00310 ( 9162) covalent geometry : angle 0.56310 (12418) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8316 (m-30) cc_final: 0.8030 (t0) REVERT: A 333 LEU cc_start: 0.9526 (pp) cc_final: 0.9164 (tt) REVERT: A 364 MET cc_start: 0.8118 (tpt) cc_final: 0.7836 (tpt) REVERT: A 492 TYR cc_start: 0.8360 (p90) cc_final: 0.7901 (p90) REVERT: A 493 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7477 (mm-30) REVERT: A 585 MET cc_start: 0.8144 (tmm) cc_final: 0.7866 (tmm) REVERT: B 340 MET cc_start: 0.8287 (mmt) cc_final: 0.7954 (mmt) REVERT: B 364 MET cc_start: 0.8643 (mpp) cc_final: 0.8345 (mpp) REVERT: B 456 ASP cc_start: 0.8784 (t0) cc_final: 0.7917 (t70) REVERT: B 481 MET cc_start: 0.8755 (ptt) cc_final: 0.8136 (pmm) REVERT: B 565 ILE cc_start: 0.9186 (mt) cc_final: 0.8949 (mm) REVERT: B 567 TYR cc_start: 0.7892 (m-10) cc_final: 0.7623 (m-80) REVERT: B 585 MET cc_start: 0.8607 (tpt) cc_final: 0.8366 (tpt) REVERT: D 20 LEU cc_start: 0.8515 (tp) cc_final: 0.8094 (tt) REVERT: D 21 LEU cc_start: 0.8627 (mt) cc_final: 0.7984 (mt) REVERT: D 35 LEU cc_start: 0.9115 (mt) cc_final: 0.8869 (mt) REVERT: D 191 HIS cc_start: 0.9468 (m90) cc_final: 0.8918 (m90) REVERT: D 220 PHE cc_start: 0.9027 (t80) cc_final: 0.8204 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1944 time to fit residues: 32.1854 Evaluate side-chains 84 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.089370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.065750 restraints weight = 40840.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067713 restraints weight = 24130.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069175 restraints weight = 16920.782| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9163 Z= 0.116 Angle : 0.541 7.739 12420 Z= 0.277 Chirality : 0.044 0.142 1374 Planarity : 0.004 0.032 1582 Dihedral : 8.272 88.167 1431 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1124 helix: 0.49 (0.29), residues: 341 sheet: -0.62 (0.36), residues: 201 loop : -0.80 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 434 HIS 0.003 0.001 HIS A 454 PHE 0.029 0.001 PHE D 227 TYR 0.024 0.001 TYR A 347 ARG 0.002 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 302) hydrogen bonds : angle 5.42687 ( 861) SS BOND : bond 0.00697 ( 1) SS BOND : angle 2.23068 ( 2) covalent geometry : bond 0.00253 ( 9162) covalent geometry : angle 0.54059 (12418) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8285 (m-30) cc_final: 0.8038 (t0) REVERT: A 333 LEU cc_start: 0.9491 (pp) cc_final: 0.9146 (tt) REVERT: A 353 MET cc_start: 0.9482 (ppp) cc_final: 0.9270 (ppp) REVERT: A 364 MET cc_start: 0.8074 (tpt) cc_final: 0.7805 (tpt) REVERT: A 492 TYR cc_start: 0.8353 (p90) cc_final: 0.7827 (p90) REVERT: A 493 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 364 MET cc_start: 0.8580 (mpp) cc_final: 0.8301 (mpp) REVERT: B 456 ASP cc_start: 0.8656 (t0) cc_final: 0.8043 (t70) REVERT: B 481 MET cc_start: 0.8711 (ptt) cc_final: 0.8500 (ptp) REVERT: B 567 TYR cc_start: 0.7839 (m-10) cc_final: 0.7583 (m-80) REVERT: D 20 LEU cc_start: 0.8499 (tp) cc_final: 0.8122 (tt) REVERT: D 21 LEU cc_start: 0.8636 (mt) cc_final: 0.7995 (mt) REVERT: D 35 LEU cc_start: 0.9036 (mt) cc_final: 0.8700 (mt) REVERT: D 191 HIS cc_start: 0.9509 (m90) cc_final: 0.8970 (m90) REVERT: D 220 PHE cc_start: 0.9017 (t80) cc_final: 0.8225 (t80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1930 time to fit residues: 34.0642 Evaluate side-chains 88 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 ASN B 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.088932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.064605 restraints weight = 40687.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066486 restraints weight = 24379.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067790 restraints weight = 17180.843| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9163 Z= 0.134 Angle : 0.561 7.594 12420 Z= 0.284 Chirality : 0.044 0.141 1374 Planarity : 0.004 0.034 1582 Dihedral : 8.231 89.306 1431 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1124 helix: 0.44 (0.28), residues: 351 sheet: -0.63 (0.35), residues: 200 loop : -0.82 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 579 HIS 0.003 0.001 HIS A 454 PHE 0.014 0.001 PHE D 238 TYR 0.019 0.001 TYR B 476 ARG 0.010 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 302) hydrogen bonds : angle 5.36663 ( 861) SS BOND : bond 0.00452 ( 1) SS BOND : angle 1.88866 ( 2) covalent geometry : bond 0.00296 ( 9162) covalent geometry : angle 0.56080 (12418) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8341 (m-30) cc_final: 0.8019 (t0) REVERT: A 315 LEU cc_start: 0.9613 (mt) cc_final: 0.9319 (mt) REVERT: A 333 LEU cc_start: 0.9525 (pp) cc_final: 0.9169 (tt) REVERT: A 364 MET cc_start: 0.8028 (tpt) cc_final: 0.7699 (tpt) REVERT: A 492 TYR cc_start: 0.8482 (p90) cc_final: 0.7939 (p90) REVERT: A 493 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 585 MET cc_start: 0.8085 (tmm) cc_final: 0.7869 (tmm) REVERT: B 364 MET cc_start: 0.8623 (mpp) cc_final: 0.8319 (mpp) REVERT: B 456 ASP cc_start: 0.8747 (t0) cc_final: 0.8135 (t70) REVERT: D 20 LEU cc_start: 0.8505 (tp) cc_final: 0.8079 (tt) REVERT: D 21 LEU cc_start: 0.8691 (mt) cc_final: 0.8045 (mt) REVERT: D 35 LEU cc_start: 0.8960 (mt) cc_final: 0.8699 (mt) REVERT: D 152 TYR cc_start: 0.6630 (m-80) cc_final: 0.6308 (m-80) REVERT: D 191 HIS cc_start: 0.9498 (m90) cc_final: 0.8938 (m90) REVERT: D 220 PHE cc_start: 0.9013 (t80) cc_final: 0.8233 (t80) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2208 time to fit residues: 37.2556 Evaluate side-chains 89 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 0.0570 overall best weight: 1.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.065275 restraints weight = 41738.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067286 restraints weight = 24630.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068756 restraints weight = 17198.693| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9163 Z= 0.125 Angle : 0.574 9.055 12420 Z= 0.293 Chirality : 0.044 0.140 1374 Planarity : 0.004 0.084 1582 Dihedral : 8.141 88.971 1431 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1124 helix: 0.43 (0.29), residues: 350 sheet: -0.59 (0.36), residues: 198 loop : -0.87 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 483 HIS 0.003 0.001 HIS B 454 PHE 0.035 0.001 PHE D 227 TYR 0.014 0.001 TYR A 347 ARG 0.006 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 302) hydrogen bonds : angle 5.43198 ( 861) SS BOND : bond 0.00291 ( 1) SS BOND : angle 1.32858 ( 2) covalent geometry : bond 0.00277 ( 9162) covalent geometry : angle 0.57419 (12418) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8311 (m-30) cc_final: 0.8028 (t0) REVERT: A 333 LEU cc_start: 0.9549 (pp) cc_final: 0.9082 (tt) REVERT: A 364 MET cc_start: 0.7946 (tpt) cc_final: 0.7582 (tpt) REVERT: A 456 ASP cc_start: 0.7771 (t70) cc_final: 0.7046 (t70) REVERT: A 492 TYR cc_start: 0.8389 (p90) cc_final: 0.7764 (p90) REVERT: B 364 MET cc_start: 0.8752 (mpp) cc_final: 0.8495 (mpp) REVERT: B 456 ASP cc_start: 0.8582 (t0) cc_final: 0.8037 (t70) REVERT: B 567 TYR cc_start: 0.7966 (m-10) cc_final: 0.7680 (m-80) REVERT: D 20 LEU cc_start: 0.8540 (tp) cc_final: 0.8179 (tt) REVERT: D 21 LEU cc_start: 0.8649 (mt) cc_final: 0.7998 (mt) REVERT: D 35 LEU cc_start: 0.9071 (mt) cc_final: 0.8805 (mt) REVERT: D 191 HIS cc_start: 0.9497 (m90) cc_final: 0.8938 (m90) REVERT: D 220 PHE cc_start: 0.9008 (t80) cc_final: 0.8222 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2173 time to fit residues: 37.8567 Evaluate side-chains 86 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 chunk 96 optimal weight: 5.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.088900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065419 restraints weight = 41413.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067398 restraints weight = 24762.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068844 restraints weight = 17262.357| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9163 Z= 0.120 Angle : 0.590 8.793 12420 Z= 0.298 Chirality : 0.045 0.159 1374 Planarity : 0.004 0.056 1582 Dihedral : 8.019 86.664 1431 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1124 helix: 0.36 (0.28), residues: 350 sheet: -0.62 (0.36), residues: 194 loop : -0.84 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 483 HIS 0.003 0.001 HIS A 454 PHE 0.014 0.001 PHE D 238 TYR 0.012 0.001 TYR D 201 ARG 0.004 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 302) hydrogen bonds : angle 5.39761 ( 861) SS BOND : bond 0.00345 ( 1) SS BOND : angle 1.13266 ( 2) covalent geometry : bond 0.00265 ( 9162) covalent geometry : angle 0.59036 (12418) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8300 (m-30) cc_final: 0.8014 (t0) REVERT: A 333 LEU cc_start: 0.9534 (pp) cc_final: 0.9142 (tt) REVERT: A 353 MET cc_start: 0.9444 (ppp) cc_final: 0.9199 (ppp) REVERT: A 364 MET cc_start: 0.7986 (tpt) cc_final: 0.7580 (tpt) REVERT: A 469 MET cc_start: 0.8345 (mmm) cc_final: 0.7436 (mmm) REVERT: A 481 MET cc_start: 0.8166 (pmm) cc_final: 0.7865 (pmm) REVERT: A 585 MET cc_start: 0.8028 (tmm) cc_final: 0.7788 (tmm) REVERT: B 364 MET cc_start: 0.8715 (mpp) cc_final: 0.8453 (mpp) REVERT: B 456 ASP cc_start: 0.8533 (t0) cc_final: 0.8006 (t70) REVERT: D 20 LEU cc_start: 0.8497 (tp) cc_final: 0.8192 (tt) REVERT: D 21 LEU cc_start: 0.8647 (mt) cc_final: 0.7985 (mt) REVERT: D 35 LEU cc_start: 0.8961 (mt) cc_final: 0.8700 (mt) REVERT: D 191 HIS cc_start: 0.9504 (m90) cc_final: 0.8943 (m90) REVERT: D 220 PHE cc_start: 0.9012 (t80) cc_final: 0.8230 (t80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2138 time to fit residues: 37.5329 Evaluate side-chains 90 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 30.0000 chunk 94 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 49 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.088926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065059 restraints weight = 41616.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067008 restraints weight = 24789.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.068449 restraints weight = 17465.344| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9163 Z= 0.127 Angle : 0.596 9.336 12420 Z= 0.300 Chirality : 0.045 0.149 1374 Planarity : 0.004 0.052 1582 Dihedral : 7.977 84.083 1431 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1124 helix: 0.38 (0.28), residues: 349 sheet: -0.46 (0.38), residues: 182 loop : -0.89 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 434 HIS 0.002 0.001 HIS B 454 PHE 0.032 0.001 PHE D 227 TYR 0.020 0.001 TYR B 476 ARG 0.004 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 302) hydrogen bonds : angle 5.39678 ( 861) SS BOND : bond 0.00325 ( 1) SS BOND : angle 1.44773 ( 2) covalent geometry : bond 0.00282 ( 9162) covalent geometry : angle 0.59602 (12418) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8305 (m-30) cc_final: 0.8002 (t0) REVERT: A 333 LEU cc_start: 0.9541 (pp) cc_final: 0.9159 (tt) REVERT: A 353 MET cc_start: 0.9471 (ppp) cc_final: 0.9241 (ppp) REVERT: A 364 MET cc_start: 0.8454 (tpt) cc_final: 0.7732 (tpt) REVERT: A 481 MET cc_start: 0.8139 (pmm) cc_final: 0.7803 (pmm) REVERT: A 585 MET cc_start: 0.8008 (tmm) cc_final: 0.7782 (tmm) REVERT: B 364 MET cc_start: 0.8717 (mpp) cc_final: 0.8433 (mpp) REVERT: B 456 ASP cc_start: 0.8583 (t0) cc_final: 0.8046 (t70) REVERT: D 20 LEU cc_start: 0.8582 (tp) cc_final: 0.8299 (tt) REVERT: D 21 LEU cc_start: 0.8663 (mt) cc_final: 0.7993 (mt) REVERT: D 35 LEU cc_start: 0.9072 (mt) cc_final: 0.8808 (mt) REVERT: D 191 HIS cc_start: 0.9488 (m90) cc_final: 0.8936 (m90) REVERT: D 220 PHE cc_start: 0.9007 (t80) cc_final: 0.8208 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3071 time to fit residues: 50.7551 Evaluate side-chains 86 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 6.9990 chunk 104 optimal weight: 0.0770 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 82 optimal weight: 0.0670 chunk 6 optimal weight: 7.9990 chunk 108 optimal weight: 0.0070 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 overall best weight: 0.1698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.090908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067024 restraints weight = 41128.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.069035 restraints weight = 24492.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070492 restraints weight = 17158.754| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9163 Z= 0.107 Angle : 0.593 9.410 12420 Z= 0.299 Chirality : 0.046 0.193 1374 Planarity : 0.004 0.044 1582 Dihedral : 7.824 82.429 1431 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1124 helix: 0.36 (0.28), residues: 343 sheet: -0.38 (0.38), residues: 183 loop : -0.84 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 434 HIS 0.003 0.000 HIS B 454 PHE 0.031 0.001 PHE A 144 TYR 0.019 0.001 TYR B 476 ARG 0.002 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 302) hydrogen bonds : angle 5.30871 ( 861) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.77010 ( 2) covalent geometry : bond 0.00232 ( 9162) covalent geometry : angle 0.59334 (12418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3697.21 seconds wall clock time: 68 minutes 59.89 seconds (4139.89 seconds total)