Starting phenix.real_space_refine on Tue Mar 3 22:14:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p6j_20264/03_2026/6p6j_20264.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p6j_20264/03_2026/6p6j_20264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p6j_20264/03_2026/6p6j_20264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p6j_20264/03_2026/6p6j_20264.map" model { file = "/net/cci-nas-00/data/ceres_data/6p6j_20264/03_2026/6p6j_20264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p6j_20264/03_2026/6p6j_20264.cif" } resolution = 3.4 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic. 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 Fe 1 7.16 5 S 46 5.16 5 C 5683 2.51 5 N 1554 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8841 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4413 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 545} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 4396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4396 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 549} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' FE': 1, 'O34': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.55, per 1000 atoms: 0.29 Number of scatterers: 8841 At special positions: 0 Unit cell: (77.76, 94.176, 132.192, 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) Fe 1 26.01 S 46 16.00 O 1557 8.00 N 1554 7.00 C 5683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 378.9 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 69.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 24 through 58 removed outlier: 3.654A pdb=" N LEU A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 109 removed outlier: 4.177A pdb=" N GLN A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 removed outlier: 3.683A pdb=" N SER A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 139 removed outlier: 5.033A pdb=" N VAL A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 163 Proline residue: A 152 - end of helix removed outlier: 4.430A pdb=" N ILE A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 188 removed outlier: 3.927A pdb=" N THR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 220 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 222 through 258 removed outlier: 3.980A pdb=" N ALA A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 277 removed outlier: 4.229A pdb=" N THR A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 300 removed outlier: 4.431A pdb=" N ALA A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 304 through 324 removed outlier: 4.170A pdb=" N GLN A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 446 through 454 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.598A pdb=" N ASN A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.683A pdb=" N GLN A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 527 Processing helix chain 'A' and resid 561 through 569 removed outlier: 3.756A pdb=" N GLY A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 removed outlier: 4.034A pdb=" N ARG A 574 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.815A pdb=" N TRP B 16 " --> pdb=" O TRP B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 59 removed outlier: 4.196A pdb=" N TYR B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 62 through 94 removed outlier: 4.356A pdb=" N ALA B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 114 removed outlier: 3.563A pdb=" N GLN B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.658A pdb=" N LEU B 119 " --> pdb=" O PRO B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 136 removed outlier: 4.280A pdb=" N MET B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 141 through 147 Processing helix chain 'B' and resid 147 through 167 Proline residue: B 156 - end of helix removed outlier: 4.418A pdb=" N TRP B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.505A pdb=" N ILE B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 188 through 216 removed outlier: 3.927A pdb=" N MET B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 225 through 251 removed outlier: 3.748A pdb=" N GLN B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.653A pdb=" N THR B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 4.013A pdb=" N VAL B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.560A pdb=" N MET B 301 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 4.041A pdb=" N GLY B 358 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 391 Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.565A pdb=" N VAL B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.514A pdb=" N LYS B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.685A pdb=" N ASN B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 571 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 367 removed outlier: 7.401A pdb=" N ALA A 359 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS A 350 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN A 361 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER A 348 " --> pdb=" O GLN A 361 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL A 363 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 406 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 422 Processing sheet with id=AA3, first strand: chain 'B' and resid 361 through 364 removed outlier: 5.335A pdb=" N ASN B 362 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B 351 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 364 removed outlier: 5.335A pdb=" N ASN B 362 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B 351 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 349 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN B 399 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 407 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 424 removed outlier: 6.253A pdb=" N SER B 422 " --> pdb=" O ILE B 504 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N MET B 373 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LEU B 550 " --> pdb=" O MET B 373 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA B 375 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET B 552 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 377 " --> pdb=" O MET B 552 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.10 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: 2912 1.34 - 1.46: 1967 1.46 - 1.58: 4056 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 9023 Sorted by residual: bond pdb=" C17 O34 A 701 " pdb=" S3 O34 A 701 " ideal model delta sigma weight residual 1.805 1.742 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C MET A 213 " pdb=" N PRO A 214 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.20e-02 6.94e+03 9.63e+00 bond pdb=" C THR A 142 " pdb=" N PRO A 143 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.92e+00 bond pdb=" C19 O34 A 701 " pdb=" C21 O34 A 701 " ideal model delta sigma weight residual 1.583 1.535 0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" CB THR B 163 " pdb=" CG2 THR B 163 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.71e+00 ... (remaining 9018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 11695 2.38 - 4.77: 496 4.77 - 7.15: 74 7.15 - 9.53: 14 9.53 - 11.91: 2 Bond angle restraints: 12281 Sorted by residual: angle pdb=" N ALA A 340 " pdb=" CA ALA A 340 " pdb=" CB ALA A 340 " ideal model delta sigma weight residual 114.17 106.64 7.53 1.14e+00 7.69e-01 4.36e+01 angle pdb=" C VAL A 456 " pdb=" N ALA A 457 " pdb=" CA ALA A 457 " ideal model delta sigma weight residual 121.19 129.32 -8.13 1.59e+00 3.96e-01 2.61e+01 angle pdb=" C LEU B 430 " pdb=" N PHE B 431 " pdb=" CA PHE B 431 " ideal model delta sigma weight residual 121.54 130.76 -9.22 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C TRP A 585 " pdb=" N VAL A 586 " pdb=" CA VAL A 586 " ideal model delta sigma weight residual 120.33 124.11 -3.78 8.00e-01 1.56e+00 2.23e+01 angle pdb=" N ASN A 427 " pdb=" CA ASN A 427 " pdb=" C ASN A 427 " ideal model delta sigma weight residual 110.91 116.12 -5.21 1.17e+00 7.31e-01 1.99e+01 ... (remaining 12276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.10: 5168 29.10 - 58.19: 226 58.19 - 87.29: 16 87.29 - 116.38: 3 116.38 - 145.48: 1 Dihedral angle restraints: 5414 sinusoidal: 2121 harmonic: 3293 Sorted by residual: dihedral pdb=" CA ASP A 432 " pdb=" C ASP A 432 " pdb=" N THR A 433 " pdb=" CA THR A 433 " ideal model delta harmonic sigma weight residual -180.00 -124.85 -55.15 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA VAL A 456 " pdb=" C VAL A 456 " pdb=" N ALA A 457 " pdb=" CA ALA A 457 " ideal model delta harmonic sigma weight residual -180.00 -140.58 -39.42 0 5.00e+00 4.00e-02 6.22e+01 dihedral pdb=" CA GLU A 339 " pdb=" C GLU A 339 " pdb=" N ALA A 340 " pdb=" CA ALA A 340 " ideal model delta harmonic sigma weight residual 180.00 145.13 34.87 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1310 0.097 - 0.195: 116 0.195 - 0.292: 9 0.292 - 0.389: 2 0.389 - 0.486: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C12 O34 A 701 " pdb=" C11 O34 A 701 " pdb=" C13 O34 A 701 " pdb=" N2 O34 A 701 " both_signs ideal model delta sigma weight residual False -2.27 -2.76 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA LEU B 430 " pdb=" N LEU B 430 " pdb=" C LEU B 430 " pdb=" CB LEU B 430 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CB ILE B 514 " pdb=" CA ILE B 514 " pdb=" CG1 ILE B 514 " pdb=" CG2 ILE B 514 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1435 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 126 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C VAL A 126 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 126 " 0.018 2.00e-02 2.50e+03 pdb=" N MET A 127 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 O34 A 701 " -0.008 2.00e-02 2.50e+03 1.83e-02 6.67e+00 pdb=" C2 O34 A 701 " -0.010 2.00e-02 2.50e+03 pdb=" C3 O34 A 701 " -0.014 2.00e-02 2.50e+03 pdb=" C4 O34 A 701 " 0.006 2.00e-02 2.50e+03 pdb=" C5 O34 A 701 " 0.031 2.00e-02 2.50e+03 pdb=" C6 O34 A 701 " -0.011 2.00e-02 2.50e+03 pdb=" C7 O34 A 701 " -0.021 2.00e-02 2.50e+03 pdb=" O1 O34 A 701 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 500 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO B 501 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " -0.035 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 38 2.50 - 3.10: 5996 3.10 - 3.70: 14008 3.70 - 4.30: 18289 4.30 - 4.90: 30385 Nonbonded interactions: 68716 Sorted by model distance: nonbonded pdb=" O2 O34 A 701 " pdb="FE FE A 702 " model vdw 1.901 2.260 nonbonded pdb=" O1 O34 A 701 " pdb="FE FE A 702 " model vdw 1.919 2.260 nonbonded pdb=" O3 O34 A 701 " pdb="FE FE A 702 " model vdw 2.078 2.260 nonbonded pdb=" N1 O34 A 701 " pdb="FE FE A 702 " model vdw 2.084 2.340 nonbonded pdb=" N3 O34 A 701 " pdb="FE FE A 702 " model vdw 2.131 2.340 ... (remaining 68711 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.680 Find NCS groups from input model: 0.050 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.012 0.620 9025 Z= 0.925 Angle : 1.122 11.913 12281 Z= 0.644 Chirality : 0.060 0.486 1438 Planarity : 0.008 0.063 1560 Dihedral : 15.941 145.477 3284 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.77 % Allowed : 13.06 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.19), residues: 1136 helix: -2.64 (0.13), residues: 737 sheet: -1.54 (0.63), residues: 62 loop : -3.22 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 410 TYR 0.019 0.002 TYR A 229 PHE 0.028 0.002 PHE B 431 TRP 0.027 0.002 TRP A 17 HIS 0.005 0.002 HIS B 529 Details of bonding type rmsd covalent geometry : bond 0.00778 ( 9023) covalent geometry : angle 1.12188 (12281) hydrogen bonds : bond 0.15209 ( 569) hydrogen bonds : angle 6.94836 ( 1689) Misc. bond : bond 0.57635 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 276 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7209 (t) REVERT: A 145 TYR cc_start: 0.7240 (t80) cc_final: 0.6818 (t80) REVERT: A 213 MET cc_start: 0.7649 (tpp) cc_final: 0.7080 (tpp) REVERT: A 234 GLU cc_start: 0.8245 (tt0) cc_final: 0.8027 (tm-30) REVERT: A 236 TRP cc_start: 0.8935 (t60) cc_final: 0.8483 (t60) REVERT: A 308 LEU cc_start: 0.8720 (tt) cc_final: 0.8337 (tt) REVERT: A 417 MET cc_start: 0.8467 (mmp) cc_final: 0.7836 (mmt) REVERT: A 436 ASN cc_start: 0.7802 (m110) cc_final: 0.7483 (m-40) REVERT: A 501 ILE cc_start: 0.8009 (mt) cc_final: 0.7783 (tt) REVERT: B 22 SER cc_start: 0.9333 (m) cc_final: 0.8977 (p) REVERT: B 34 MET cc_start: 0.6145 (tmm) cc_final: 0.5735 (mmp) REVERT: B 43 MET cc_start: 0.8521 (tpp) cc_final: 0.8292 (mmm) REVERT: B 68 ASN cc_start: 0.8505 (m110) cc_final: 0.8111 (t0) REVERT: B 118 LYS cc_start: 0.8746 (mttp) cc_final: 0.8292 (mmmt) REVERT: B 184 PHE cc_start: 0.8029 (m-10) cc_final: 0.7610 (t80) REVERT: B 389 LYS cc_start: 0.8984 (mttt) cc_final: 0.8734 (ttmm) REVERT: B 513 ASP cc_start: 0.7714 (t0) cc_final: 0.7428 (t0) REVERT: B 522 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8456 (tppt) REVERT: B 552 MET cc_start: 0.8165 (tpp) cc_final: 0.7877 (mmm) outliers start: 7 outliers final: 3 residues processed: 279 average time/residue: 0.1005 time to fit residues: 37.6987 Evaluate side-chains 177 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 335 GLN A 436 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN A 564 GLN A 568 GLN B 18 GLN B 98 GLN B 248 HIS B 323 GLN B 416 GLN B 530 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.089177 restraints weight = 17548.894| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.48 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9025 Z= 0.161 Angle : 0.724 7.715 12281 Z= 0.371 Chirality : 0.044 0.211 1438 Planarity : 0.006 0.067 1560 Dihedral : 7.900 162.827 1294 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.95 % Allowed : 21.62 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.23), residues: 1136 helix: -0.48 (0.18), residues: 721 sheet: -0.09 (0.63), residues: 72 loop : -2.65 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 252 TYR 0.017 0.001 TYR A 351 PHE 0.028 0.002 PHE B 431 TRP 0.027 0.002 TRP B 85 HIS 0.004 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9023) covalent geometry : angle 0.72427 (12281) hydrogen bonds : bond 0.04161 ( 569) hydrogen bonds : angle 4.86195 ( 1689) Misc. bond : bond 0.00265 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8473 (tpp) cc_final: 0.8239 (tpp) REVERT: A 145 TYR cc_start: 0.7230 (t80) cc_final: 0.6788 (t80) REVERT: A 191 MET cc_start: 0.8143 (mmm) cc_final: 0.7826 (mmm) REVERT: A 213 MET cc_start: 0.7812 (tpp) cc_final: 0.7271 (tpp) REVERT: A 231 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8199 (mmp80) REVERT: A 235 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 351 TYR cc_start: 0.9086 (m-80) cc_final: 0.8877 (m-10) REVERT: A 411 MET cc_start: 0.7753 (tpt) cc_final: 0.7536 (tpt) REVERT: A 436 ASN cc_start: 0.8019 (m-40) cc_final: 0.7598 (m-40) REVERT: A 489 ILE cc_start: 0.8882 (mm) cc_final: 0.8531 (tp) REVERT: A 541 MET cc_start: 0.7437 (tpt) cc_final: 0.7077 (tpt) REVERT: B 34 MET cc_start: 0.6048 (tmm) cc_final: 0.5773 (mmp) REVERT: B 43 MET cc_start: 0.8489 (tpp) cc_final: 0.8062 (mmm) REVERT: B 68 ASN cc_start: 0.8851 (m110) cc_final: 0.8423 (t0) REVERT: B 118 LYS cc_start: 0.8437 (mttp) cc_final: 0.8059 (mmmt) REVERT: B 126 GLU cc_start: 0.7293 (mp0) cc_final: 0.6808 (mp0) REVERT: B 127 MET cc_start: 0.8721 (pmm) cc_final: 0.8416 (pmm) REVERT: B 184 PHE cc_start: 0.8341 (m-10) cc_final: 0.7458 (t80) REVERT: B 192 MET cc_start: 0.8451 (tmm) cc_final: 0.8215 (tmm) REVERT: B 343 ASP cc_start: 0.7971 (m-30) cc_final: 0.6990 (p0) REVERT: B 418 ASN cc_start: 0.8960 (m-40) cc_final: 0.8723 (m-40) REVERT: B 429 TRP cc_start: 0.6375 (OUTLIER) cc_final: 0.5911 (t60) REVERT: B 504 ILE cc_start: 0.8696 (mt) cc_final: 0.8231 (pt) REVERT: B 513 ASP cc_start: 0.8226 (t0) cc_final: 0.7886 (t0) REVERT: B 522 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8429 (tptp) REVERT: B 560 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8825 (tm-30) outliers start: 36 outliers final: 18 residues processed: 232 average time/residue: 0.0924 time to fit residues: 30.1754 Evaluate side-chains 199 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 429 TRP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 471 TRP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.089396 restraints weight = 17332.322| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.39 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9025 Z= 0.143 Angle : 0.670 7.373 12281 Z= 0.339 Chirality : 0.043 0.179 1438 Planarity : 0.004 0.053 1560 Dihedral : 7.763 176.960 1293 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.38 % Allowed : 24.04 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.25), residues: 1136 helix: 0.43 (0.19), residues: 747 sheet: 1.01 (0.70), residues: 65 loop : -2.59 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.013 0.001 TYR A 351 PHE 0.017 0.001 PHE B 431 TRP 0.025 0.001 TRP B 85 HIS 0.004 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9023) covalent geometry : angle 0.67012 (12281) hydrogen bonds : bond 0.03677 ( 569) hydrogen bonds : angle 4.44894 ( 1689) Misc. bond : bond 0.00151 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8589 (tt) cc_final: 0.8389 (tp) REVERT: A 80 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 145 TYR cc_start: 0.7230 (t80) cc_final: 0.6860 (t80) REVERT: A 191 MET cc_start: 0.8159 (mmm) cc_final: 0.7760 (mmm) REVERT: A 213 MET cc_start: 0.7697 (tpp) cc_final: 0.7249 (tpp) REVERT: A 235 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 236 TRP cc_start: 0.8658 (t60) cc_final: 0.8185 (t60) REVERT: A 411 MET cc_start: 0.7711 (tpt) cc_final: 0.7479 (tpt) REVERT: A 417 MET cc_start: 0.8534 (mmp) cc_final: 0.7592 (mmt) REVERT: A 428 PHE cc_start: 0.8252 (t80) cc_final: 0.7498 (t80) REVERT: A 436 ASN cc_start: 0.8007 (m-40) cc_final: 0.7656 (m-40) REVERT: A 489 ILE cc_start: 0.8795 (mm) cc_final: 0.8470 (tp) REVERT: A 519 LEU cc_start: 0.8829 (mt) cc_final: 0.8614 (tt) REVERT: B 29 MET cc_start: 0.7860 (mmm) cc_final: 0.7078 (mmm) REVERT: B 34 MET cc_start: 0.6119 (tmm) cc_final: 0.5743 (mmp) REVERT: B 43 MET cc_start: 0.8387 (tpp) cc_final: 0.8006 (mmm) REVERT: B 50 CYS cc_start: 0.8688 (m) cc_final: 0.8001 (t) REVERT: B 68 ASN cc_start: 0.8762 (m110) cc_final: 0.8310 (t0) REVERT: B 118 LYS cc_start: 0.8299 (mttp) cc_final: 0.7927 (mmmt) REVERT: B 126 GLU cc_start: 0.7384 (mp0) cc_final: 0.6912 (mp0) REVERT: B 127 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8505 (pmm) REVERT: B 192 MET cc_start: 0.8559 (tmm) cc_final: 0.8250 (tmm) REVERT: B 194 ARG cc_start: 0.8379 (tmm-80) cc_final: 0.8140 (ttp80) REVERT: B 343 ASP cc_start: 0.7878 (m-30) cc_final: 0.7023 (p0) REVERT: B 389 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8487 (ttmm) REVERT: B 418 ASN cc_start: 0.8949 (m-40) cc_final: 0.8672 (m-40) REVERT: B 429 TRP cc_start: 0.6156 (OUTLIER) cc_final: 0.5509 (t60) REVERT: B 503 VAL cc_start: 0.8987 (t) cc_final: 0.8667 (m) REVERT: B 504 ILE cc_start: 0.8707 (mt) cc_final: 0.8274 (pt) REVERT: B 513 ASP cc_start: 0.8229 (t0) cc_final: 0.7896 (t0) REVERT: B 522 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8343 (tppt) REVERT: B 560 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8770 (tm-30) outliers start: 49 outliers final: 29 residues processed: 228 average time/residue: 0.0890 time to fit residues: 28.7471 Evaluate side-chains 207 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 TRP Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 429 TRP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 471 TRP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.115292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089595 restraints weight = 17498.653| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.25 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9025 Z= 0.143 Angle : 0.657 8.297 12281 Z= 0.329 Chirality : 0.043 0.191 1438 Planarity : 0.004 0.038 1560 Dihedral : 7.645 179.379 1293 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.71 % Allowed : 24.48 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1136 helix: 0.88 (0.19), residues: 749 sheet: 1.24 (0.69), residues: 65 loop : -2.40 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.017 0.001 TYR B 394 PHE 0.020 0.001 PHE B 297 TRP 0.019 0.001 TRP B 85 HIS 0.004 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9023) covalent geometry : angle 0.65746 (12281) hydrogen bonds : bond 0.03523 ( 569) hydrogen bonds : angle 4.28309 ( 1689) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7908 (mp) REVERT: A 145 TYR cc_start: 0.7250 (t80) cc_final: 0.6922 (t80) REVERT: A 191 MET cc_start: 0.8363 (mmm) cc_final: 0.7951 (mmm) REVERT: A 213 MET cc_start: 0.7689 (tpp) cc_final: 0.7281 (tpp) REVERT: A 235 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 236 TRP cc_start: 0.8633 (t60) cc_final: 0.8122 (t60) REVERT: A 351 TYR cc_start: 0.8889 (m-10) cc_final: 0.8647 (m-80) REVERT: A 393 TYR cc_start: 0.7985 (m-80) cc_final: 0.7151 (m-10) REVERT: A 411 MET cc_start: 0.7735 (tpt) cc_final: 0.7517 (tpt) REVERT: A 417 MET cc_start: 0.8461 (mmp) cc_final: 0.7500 (mmp) REVERT: A 428 PHE cc_start: 0.8193 (t80) cc_final: 0.7445 (t80) REVERT: A 436 ASN cc_start: 0.8000 (m-40) cc_final: 0.7742 (m-40) REVERT: A 519 LEU cc_start: 0.8870 (mt) cc_final: 0.8661 (tt) REVERT: B 34 MET cc_start: 0.6181 (tmm) cc_final: 0.5803 (mmp) REVERT: B 43 MET cc_start: 0.8467 (tpp) cc_final: 0.8089 (mmm) REVERT: B 50 CYS cc_start: 0.8664 (m) cc_final: 0.8071 (t) REVERT: B 68 ASN cc_start: 0.8714 (m110) cc_final: 0.8339 (t0) REVERT: B 118 LYS cc_start: 0.8311 (mttp) cc_final: 0.7949 (mmmt) REVERT: B 126 GLU cc_start: 0.7422 (mp0) cc_final: 0.6948 (mp0) REVERT: B 127 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8452 (pmm) REVERT: B 192 MET cc_start: 0.8590 (tmm) cc_final: 0.8271 (tmm) REVERT: B 343 ASP cc_start: 0.7776 (m-30) cc_final: 0.7001 (p0) REVERT: B 352 ARG cc_start: 0.8413 (mtp85) cc_final: 0.7935 (mmm-85) REVERT: B 389 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8465 (ttmm) REVERT: B 429 TRP cc_start: 0.6097 (OUTLIER) cc_final: 0.5794 (t60) REVERT: B 504 ILE cc_start: 0.8717 (mt) cc_final: 0.8293 (pt) REVERT: B 513 ASP cc_start: 0.8269 (t0) cc_final: 0.7929 (t0) REVERT: B 522 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8359 (tptp) REVERT: B 560 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8746 (tm-30) outliers start: 52 outliers final: 37 residues processed: 216 average time/residue: 0.0847 time to fit residues: 26.4246 Evaluate side-chains 211 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 429 TRP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 471 TRP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 GLN B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085964 restraints weight = 17629.798| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.25 r_work: 0.3091 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9025 Z= 0.197 Angle : 0.694 8.929 12281 Z= 0.346 Chirality : 0.044 0.234 1438 Planarity : 0.004 0.037 1560 Dihedral : 7.651 177.420 1293 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 8.67 % Allowed : 22.83 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 1136 helix: 1.07 (0.19), residues: 752 sheet: 1.10 (0.68), residues: 66 loop : -2.32 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.015 0.002 TYR B 394 PHE 0.021 0.002 PHE A 462 TRP 0.020 0.002 TRP B 85 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9023) covalent geometry : angle 0.69425 (12281) hydrogen bonds : bond 0.03788 ( 569) hydrogen bonds : angle 4.32510 ( 1689) Misc. bond : bond 0.00187 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 173 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8086 (mp) REVERT: A 145 TYR cc_start: 0.7563 (t80) cc_final: 0.7265 (t80) REVERT: A 191 MET cc_start: 0.8502 (mmm) cc_final: 0.7955 (mmm) REVERT: A 213 MET cc_start: 0.7885 (tpp) cc_final: 0.7503 (tpp) REVERT: A 231 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8411 (tpp80) REVERT: A 235 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 236 TRP cc_start: 0.8793 (t60) cc_final: 0.8295 (t60) REVERT: A 411 MET cc_start: 0.7856 (tpt) cc_final: 0.7637 (tpt) REVERT: A 417 MET cc_start: 0.8655 (mmp) cc_final: 0.7683 (mmp) REVERT: A 436 ASN cc_start: 0.8011 (m-40) cc_final: 0.7778 (m-40) REVERT: A 559 MET cc_start: 0.8317 (mmm) cc_final: 0.7923 (mmm) REVERT: B 34 MET cc_start: 0.6739 (tmm) cc_final: 0.6192 (mmp) REVERT: B 50 CYS cc_start: 0.8899 (m) cc_final: 0.8345 (t) REVERT: B 118 LYS cc_start: 0.8470 (mttp) cc_final: 0.8049 (mmmt) REVERT: B 126 GLU cc_start: 0.7415 (mp0) cc_final: 0.6852 (mp0) REVERT: B 127 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8456 (pmm) REVERT: B 184 PHE cc_start: 0.8543 (m-10) cc_final: 0.7488 (t80) REVERT: B 192 MET cc_start: 0.8680 (tmm) cc_final: 0.8370 (tmm) REVERT: B 194 ARG cc_start: 0.8533 (tmm-80) cc_final: 0.8261 (ttp80) REVERT: B 343 ASP cc_start: 0.7845 (m-30) cc_final: 0.7039 (p0) REVERT: B 389 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8676 (ttmm) REVERT: B 390 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 418 ASN cc_start: 0.9036 (m-40) cc_final: 0.8809 (m-40) REVERT: B 429 TRP cc_start: 0.6412 (OUTLIER) cc_final: 0.5987 (t60) REVERT: B 504 ILE cc_start: 0.8881 (mt) cc_final: 0.8521 (pt) REVERT: B 513 ASP cc_start: 0.8420 (t0) cc_final: 0.8076 (t0) REVERT: B 522 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8398 (tptp) REVERT: B 549 ILE cc_start: 0.8970 (mm) cc_final: 0.8726 (tp) outliers start: 79 outliers final: 55 residues processed: 229 average time/residue: 0.0845 time to fit residues: 27.7729 Evaluate side-chains 221 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 TRP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 429 TRP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.115143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089371 restraints weight = 17459.014| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.24 r_work: 0.3152 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9025 Z= 0.129 Angle : 0.660 10.093 12281 Z= 0.322 Chirality : 0.044 0.277 1438 Planarity : 0.003 0.038 1560 Dihedral : 7.425 174.871 1293 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.60 % Allowed : 26.45 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1136 helix: 1.29 (0.19), residues: 748 sheet: 1.27 (0.69), residues: 66 loop : -2.32 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 106 TYR 0.015 0.002 TYR B 394 PHE 0.018 0.001 PHE B 297 TRP 0.026 0.001 TRP B 577 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9023) covalent geometry : angle 0.66020 (12281) hydrogen bonds : bond 0.03371 ( 569) hydrogen bonds : angle 4.15595 ( 1689) Misc. bond : bond 0.00132 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8952 (pt0) cc_final: 0.8670 (pt0) REVERT: A 145 TYR cc_start: 0.7531 (t80) cc_final: 0.7218 (t80) REVERT: A 191 MET cc_start: 0.8423 (mmm) cc_final: 0.7874 (mmm) REVERT: A 213 MET cc_start: 0.7883 (tpp) cc_final: 0.7495 (tpp) REVERT: A 231 ARG cc_start: 0.8657 (tpp80) cc_final: 0.8351 (tpp80) REVERT: A 235 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 236 TRP cc_start: 0.8733 (t60) cc_final: 0.8212 (t60) REVERT: A 417 MET cc_start: 0.8511 (mmp) cc_final: 0.7541 (mmp) REVERT: A 436 ASN cc_start: 0.7754 (m-40) cc_final: 0.7467 (m-40) REVERT: A 470 TYR cc_start: 0.7857 (m-80) cc_final: 0.7509 (m-80) REVERT: A 559 MET cc_start: 0.8222 (mmm) cc_final: 0.7795 (mmm) REVERT: B 34 MET cc_start: 0.6569 (tmm) cc_final: 0.6045 (mmp) REVERT: B 50 CYS cc_start: 0.8831 (m) cc_final: 0.8305 (t) REVERT: B 118 LYS cc_start: 0.8371 (mttp) cc_final: 0.7997 (mmmt) REVERT: B 126 GLU cc_start: 0.7374 (mp0) cc_final: 0.6874 (mp0) REVERT: B 127 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8597 (pmm) REVERT: B 184 PHE cc_start: 0.8432 (m-10) cc_final: 0.7359 (t80) REVERT: B 192 MET cc_start: 0.8740 (tmm) cc_final: 0.8404 (tmm) REVERT: B 194 ARG cc_start: 0.8523 (tmm-80) cc_final: 0.8256 (ttp80) REVERT: B 335 GLN cc_start: 0.7443 (pm20) cc_final: 0.7064 (pp30) REVERT: B 343 ASP cc_start: 0.7748 (m-30) cc_final: 0.6991 (p0) REVERT: B 389 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8432 (ttmm) REVERT: B 418 ASN cc_start: 0.9006 (m-40) cc_final: 0.8728 (m-40) REVERT: B 504 ILE cc_start: 0.8887 (mt) cc_final: 0.8556 (pt) REVERT: B 513 ASP cc_start: 0.8335 (t0) cc_final: 0.7940 (t0) REVERT: B 522 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8360 (tptp) outliers start: 51 outliers final: 36 residues processed: 226 average time/residue: 0.0830 time to fit residues: 27.2305 Evaluate side-chains 212 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 168 TRP Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089280 restraints weight = 17483.915| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.40 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9025 Z= 0.123 Angle : 0.655 11.036 12281 Z= 0.320 Chirality : 0.043 0.285 1438 Planarity : 0.003 0.035 1560 Dihedral : 7.321 173.218 1293 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.60 % Allowed : 26.78 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1136 helix: 1.38 (0.19), residues: 751 sheet: 0.88 (0.69), residues: 71 loop : -2.29 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 345 TYR 0.014 0.001 TYR B 394 PHE 0.015 0.001 PHE B 431 TRP 0.037 0.002 TRP B 429 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9023) covalent geometry : angle 0.65469 (12281) hydrogen bonds : bond 0.03255 ( 569) hydrogen bonds : angle 4.05287 ( 1689) Misc. bond : bond 0.00128 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8777 (tpp) cc_final: 0.8498 (mmm) REVERT: A 145 TYR cc_start: 0.7283 (t80) cc_final: 0.6938 (t80) REVERT: A 191 MET cc_start: 0.8455 (mmm) cc_final: 0.7860 (mmm) REVERT: A 213 MET cc_start: 0.7738 (tpp) cc_final: 0.7422 (tpp) REVERT: A 231 ARG cc_start: 0.8566 (tpp80) cc_final: 0.8216 (tpp80) REVERT: A 235 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 236 TRP cc_start: 0.8728 (t60) cc_final: 0.8188 (t60) REVERT: A 351 TYR cc_start: 0.8585 (m-10) cc_final: 0.8262 (m-80) REVERT: A 411 MET cc_start: 0.7988 (tpt) cc_final: 0.7739 (tpt) REVERT: A 417 MET cc_start: 0.8242 (mmp) cc_final: 0.7248 (mmp) REVERT: A 470 TYR cc_start: 0.7743 (m-80) cc_final: 0.7449 (m-80) REVERT: B 29 MET cc_start: 0.8050 (mmm) cc_final: 0.7364 (mmm) REVERT: B 34 MET cc_start: 0.6444 (tmm) cc_final: 0.6024 (mmp) REVERT: B 50 CYS cc_start: 0.8583 (m) cc_final: 0.8236 (t) REVERT: B 118 LYS cc_start: 0.8351 (mttp) cc_final: 0.8013 (mmmt) REVERT: B 126 GLU cc_start: 0.7273 (mp0) cc_final: 0.6831 (mp0) REVERT: B 127 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8454 (pmm) REVERT: B 184 PHE cc_start: 0.8360 (m-10) cc_final: 0.7360 (t80) REVERT: B 192 MET cc_start: 0.8625 (tmm) cc_final: 0.8239 (tmm) REVERT: B 194 ARG cc_start: 0.8497 (tmm-80) cc_final: 0.8248 (ttp80) REVERT: B 299 GLU cc_start: 0.8549 (tt0) cc_final: 0.8207 (mt-10) REVERT: B 303 MET cc_start: 0.8253 (mmp) cc_final: 0.8037 (mmt) REVERT: B 335 GLN cc_start: 0.7536 (pm20) cc_final: 0.7208 (pp30) REVERT: B 343 ASP cc_start: 0.7600 (m-30) cc_final: 0.6916 (p0) REVERT: B 389 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8406 (ttmm) REVERT: B 418 ASN cc_start: 0.9013 (m-40) cc_final: 0.8754 (m-40) REVERT: B 436 LEU cc_start: 0.7210 (mm) cc_final: 0.6764 (tt) REVERT: B 504 ILE cc_start: 0.8796 (mt) cc_final: 0.8506 (pt) REVERT: B 513 ASP cc_start: 0.8199 (t0) cc_final: 0.7854 (t0) REVERT: B 522 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8317 (tptp) outliers start: 51 outliers final: 42 residues processed: 218 average time/residue: 0.0779 time to fit residues: 25.0795 Evaluate side-chains 219 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.0020 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.115763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089667 restraints weight = 17074.203| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.26 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9025 Z= 0.120 Angle : 0.653 10.934 12281 Z= 0.319 Chirality : 0.043 0.296 1438 Planarity : 0.003 0.038 1560 Dihedral : 7.230 172.617 1293 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.60 % Allowed : 27.66 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.26), residues: 1136 helix: 1.45 (0.19), residues: 752 sheet: 0.78 (0.68), residues: 71 loop : -2.24 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.013 0.001 TYR A 272 PHE 0.023 0.001 PHE B 431 TRP 0.036 0.001 TRP B 429 HIS 0.002 0.000 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9023) covalent geometry : angle 0.65259 (12281) hydrogen bonds : bond 0.03202 ( 569) hydrogen bonds : angle 3.97008 ( 1689) Misc. bond : bond 0.00123 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8756 (tpp) cc_final: 0.8456 (mmm) REVERT: A 46 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 145 TYR cc_start: 0.7380 (t80) cc_final: 0.7128 (t80) REVERT: A 176 PHE cc_start: 0.7345 (t80) cc_final: 0.7130 (t80) REVERT: A 191 MET cc_start: 0.8483 (mmm) cc_final: 0.7841 (mmm) REVERT: A 213 MET cc_start: 0.7750 (tpp) cc_final: 0.7432 (tpp) REVERT: A 231 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8210 (tpp80) REVERT: A 235 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 236 TRP cc_start: 0.8726 (t60) cc_final: 0.8207 (t60) REVERT: A 302 MET cc_start: 0.7946 (tpt) cc_final: 0.7638 (tmm) REVERT: A 338 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5805 (tm-30) REVERT: A 411 MET cc_start: 0.7953 (tpt) cc_final: 0.7629 (tpt) REVERT: A 417 MET cc_start: 0.8185 (mmp) cc_final: 0.7195 (mmp) REVERT: A 424 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8157 (m-80) REVERT: A 470 TYR cc_start: 0.7780 (m-80) cc_final: 0.7481 (m-80) REVERT: A 559 MET cc_start: 0.7948 (mmm) cc_final: 0.7546 (mmm) REVERT: B 34 MET cc_start: 0.6407 (tmm) cc_final: 0.5947 (mmp) REVERT: B 50 CYS cc_start: 0.8648 (m) cc_final: 0.8266 (t) REVERT: B 118 LYS cc_start: 0.8380 (mttp) cc_final: 0.8003 (mmmt) REVERT: B 126 GLU cc_start: 0.7220 (mp0) cc_final: 0.6781 (mp0) REVERT: B 127 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8430 (pmm) REVERT: B 184 PHE cc_start: 0.8371 (m-10) cc_final: 0.7382 (t80) REVERT: B 192 MET cc_start: 0.8672 (tmm) cc_final: 0.8277 (tmm) REVERT: B 194 ARG cc_start: 0.8538 (tmm-80) cc_final: 0.8307 (ttp80) REVERT: B 299 GLU cc_start: 0.8494 (tt0) cc_final: 0.8195 (mt-10) REVERT: B 335 GLN cc_start: 0.7627 (pm20) cc_final: 0.7248 (pp30) REVERT: B 343 ASP cc_start: 0.7535 (m-30) cc_final: 0.6857 (p0) REVERT: B 372 SER cc_start: 0.8357 (t) cc_final: 0.7938 (p) REVERT: B 389 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8446 (ttmm) REVERT: B 436 LEU cc_start: 0.7048 (mm) cc_final: 0.6600 (tt) REVERT: B 504 ILE cc_start: 0.8793 (mt) cc_final: 0.8518 (pt) REVERT: B 513 ASP cc_start: 0.8141 (t0) cc_final: 0.7891 (t0) REVERT: B 522 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8333 (tptp) outliers start: 51 outliers final: 38 residues processed: 216 average time/residue: 0.0760 time to fit residues: 24.4709 Evaluate side-chains 217 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089495 restraints weight = 17312.179| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 4.27 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9025 Z= 0.139 Angle : 0.669 11.203 12281 Z= 0.326 Chirality : 0.044 0.302 1438 Planarity : 0.003 0.037 1560 Dihedral : 7.232 172.200 1293 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.27 % Allowed : 28.76 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1136 helix: 1.53 (0.19), residues: 748 sheet: 1.22 (0.68), residues: 66 loop : -2.27 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.012 0.001 TYR B 394 PHE 0.020 0.001 PHE B 297 TRP 0.027 0.001 TRP B 429 HIS 0.002 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9023) covalent geometry : angle 0.66891 (12281) hydrogen bonds : bond 0.03264 ( 569) hydrogen bonds : angle 3.94985 ( 1689) Misc. bond : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8754 (tpp) cc_final: 0.8448 (mmm) REVERT: A 46 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8127 (tt) REVERT: A 145 TYR cc_start: 0.7363 (t80) cc_final: 0.7116 (t80) REVERT: A 176 PHE cc_start: 0.7329 (t80) cc_final: 0.7102 (t80) REVERT: A 191 MET cc_start: 0.8502 (mmm) cc_final: 0.7827 (mmm) REVERT: A 213 MET cc_start: 0.7761 (tpp) cc_final: 0.7472 (tpp) REVERT: A 231 ARG cc_start: 0.8536 (tpp80) cc_final: 0.8167 (tpp80) REVERT: A 235 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 236 TRP cc_start: 0.8685 (t60) cc_final: 0.8154 (t60) REVERT: A 302 MET cc_start: 0.7904 (tpt) cc_final: 0.7663 (tmm) REVERT: A 411 MET cc_start: 0.7980 (tpt) cc_final: 0.7631 (tpt) REVERT: A 417 MET cc_start: 0.8194 (mmp) cc_final: 0.7167 (mmp) REVERT: A 424 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: A 470 TYR cc_start: 0.7717 (m-80) cc_final: 0.7448 (m-80) REVERT: A 559 MET cc_start: 0.8148 (mmm) cc_final: 0.7767 (mmm) REVERT: B 34 MET cc_start: 0.6310 (tmm) cc_final: 0.5758 (mmp) REVERT: B 50 CYS cc_start: 0.8601 (m) cc_final: 0.8232 (t) REVERT: B 118 LYS cc_start: 0.8352 (mttp) cc_final: 0.7984 (mmmt) REVERT: B 126 GLU cc_start: 0.7313 (mp0) cc_final: 0.6874 (mp0) REVERT: B 127 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8461 (pmm) REVERT: B 184 PHE cc_start: 0.8375 (m-10) cc_final: 0.7388 (t80) REVERT: B 192 MET cc_start: 0.8645 (tmm) cc_final: 0.8241 (tmm) REVERT: B 194 ARG cc_start: 0.8522 (tmm-80) cc_final: 0.8295 (ttp80) REVERT: B 299 GLU cc_start: 0.8635 (tt0) cc_final: 0.8051 (mt-10) REVERT: B 335 GLN cc_start: 0.7689 (pm20) cc_final: 0.7288 (pp30) REVERT: B 343 ASP cc_start: 0.7534 (m-30) cc_final: 0.6861 (p0) REVERT: B 372 SER cc_start: 0.8335 (t) cc_final: 0.7930 (p) REVERT: B 389 LYS cc_start: 0.8829 (ttmt) cc_final: 0.8450 (ttmm) REVERT: B 436 LEU cc_start: 0.6994 (mm) cc_final: 0.6542 (tt) REVERT: B 504 ILE cc_start: 0.8772 (mt) cc_final: 0.8491 (pt) REVERT: B 513 ASP cc_start: 0.8219 (t0) cc_final: 0.7954 (t0) REVERT: B 522 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8321 (tptp) outliers start: 48 outliers final: 40 residues processed: 208 average time/residue: 0.0756 time to fit residues: 23.4747 Evaluate side-chains 219 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.117077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090938 restraints weight = 17308.328| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 4.27 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9025 Z= 0.123 Angle : 0.654 11.862 12281 Z= 0.318 Chirality : 0.043 0.303 1438 Planarity : 0.003 0.034 1560 Dihedral : 7.172 171.503 1293 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.94 % Allowed : 28.54 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.26), residues: 1136 helix: 1.55 (0.19), residues: 748 sheet: 1.19 (0.69), residues: 66 loop : -2.22 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.013 0.001 TYR B 394 PHE 0.020 0.001 PHE B 431 TRP 0.025 0.001 TRP B 429 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9023) covalent geometry : angle 0.65357 (12281) hydrogen bonds : bond 0.03158 ( 569) hydrogen bonds : angle 3.91879 ( 1689) Misc. bond : bond 0.00124 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8760 (tpp) cc_final: 0.8455 (mmm) REVERT: A 46 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8109 (tt) REVERT: A 145 TYR cc_start: 0.7315 (t80) cc_final: 0.7082 (t80) REVERT: A 176 PHE cc_start: 0.7334 (t80) cc_final: 0.7122 (t80) REVERT: A 191 MET cc_start: 0.8503 (mmm) cc_final: 0.7751 (mmm) REVERT: A 213 MET cc_start: 0.7731 (tpp) cc_final: 0.7452 (tpp) REVERT: A 231 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8176 (tpp80) REVERT: A 235 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 236 TRP cc_start: 0.8672 (t60) cc_final: 0.8163 (t60) REVERT: A 270 SER cc_start: 0.9075 (t) cc_final: 0.8858 (p) REVERT: A 302 MET cc_start: 0.7656 (tpt) cc_final: 0.7188 (tmm) REVERT: A 338 GLN cc_start: 0.5836 (OUTLIER) cc_final: 0.5479 (tm-30) REVERT: A 393 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: A 411 MET cc_start: 0.8002 (tpt) cc_final: 0.7667 (tpt) REVERT: A 417 MET cc_start: 0.8119 (mmp) cc_final: 0.7082 (mmp) REVERT: A 426 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7882 (t70) REVERT: A 470 TYR cc_start: 0.7720 (m-80) cc_final: 0.7455 (m-80) REVERT: B 34 MET cc_start: 0.6158 (tmm) cc_final: 0.5508 (mmp) REVERT: B 50 CYS cc_start: 0.8467 (m) cc_final: 0.8148 (t) REVERT: B 118 LYS cc_start: 0.8332 (mttp) cc_final: 0.7949 (mmmt) REVERT: B 126 GLU cc_start: 0.7284 (mp0) cc_final: 0.6860 (mp0) REVERT: B 127 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8449 (pmm) REVERT: B 192 MET cc_start: 0.8649 (tmm) cc_final: 0.8264 (tmm) REVERT: B 299 GLU cc_start: 0.8548 (tt0) cc_final: 0.8049 (mt-10) REVERT: B 322 GLU cc_start: 0.8968 (tp30) cc_final: 0.8255 (tp30) REVERT: B 335 GLN cc_start: 0.7729 (pm20) cc_final: 0.7326 (pp30) REVERT: B 343 ASP cc_start: 0.7468 (m-30) cc_final: 0.6713 (p0) REVERT: B 372 SER cc_start: 0.8218 (t) cc_final: 0.7839 (p) REVERT: B 389 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8452 (ttmm) REVERT: B 436 LEU cc_start: 0.6991 (mm) cc_final: 0.6501 (tt) REVERT: B 504 ILE cc_start: 0.8763 (mt) cc_final: 0.8491 (pt) REVERT: B 513 ASP cc_start: 0.8252 (t0) cc_final: 0.8003 (t0) REVERT: B 522 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8301 (tptp) outliers start: 45 outliers final: 36 residues processed: 215 average time/residue: 0.0776 time to fit residues: 24.8498 Evaluate side-chains 218 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090748 restraints weight = 17140.562| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.25 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9025 Z= 0.128 Angle : 0.667 11.859 12281 Z= 0.323 Chirality : 0.043 0.308 1438 Planarity : 0.003 0.032 1560 Dihedral : 7.173 171.225 1293 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.27 % Allowed : 28.32 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1136 helix: 1.60 (0.19), residues: 748 sheet: 1.18 (0.69), residues: 66 loop : -2.21 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 499 TYR 0.015 0.001 TYR A 272 PHE 0.017 0.001 PHE B 431 TRP 0.023 0.001 TRP B 577 HIS 0.002 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9023) covalent geometry : angle 0.66714 (12281) hydrogen bonds : bond 0.03175 ( 569) hydrogen bonds : angle 3.88687 ( 1689) Misc. bond : bond 0.00104 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.16 seconds wall clock time: 29 minutes 19.16 seconds (1759.16 seconds total)