Starting phenix.real_space_refine on Fri Jul 3 01:38:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zrh_14914/07_2026/7zrh_14914.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrh_14914/07_2026/7zrh_14914.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7zrh_14914/07_2026/7zrh_14914.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zrh_14914/07_2026/7zrh_14914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zrh_14914/07_2026/7zrh_14914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrh_14914/07_2026/7zrh_14914.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrh_14914/07_2026/7zrh_14914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrh_14914/07_2026/7zrh_14914.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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 7 8.98 5 P 5 5.49 5 S 62 5.16 5 C 7123 2.51 5 N 1822 2.21 5 O 1995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11014 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5021 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {' K': 6, 'CDL': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {' K': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.89, per 1000 atoms: 0.26 Number of scatterers: 11014 At special positions: 0 Unit cell: (89.056, 115.368, 144.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 7 19.00 S 62 16.00 P 5 15.00 O 1995 8.00 N 1822 7.00 C 7123 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=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 573.0 milliseconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 62.8% alpha, 5.3% 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 1 through 32 removed outlier: 3.802A pdb=" N GLY A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.756A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 removed outlier: 4.103A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.625A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 133 through 157 removed outlier: 3.694A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.639A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.923A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.388A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.730A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 304 removed outlier: 4.423A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.473A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.573A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 removed outlier: 4.172A pdb=" N LEU A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 436 removed outlier: 4.562A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 523 through 542 removed outlier: 4.282A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.554A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.729A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.519A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.981A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 98 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.632A pdb=" N PHE B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 284 removed outlier: 5.892A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.650A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.822A pdb=" N LEU B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.674A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.875A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.636A pdb=" N GLN B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 582 removed outlier: 3.660A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Proline residue: B 592 - end of helix removed outlier: 3.616A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 removed outlier: 3.888A pdb=" N ILE B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.099A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.073A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.576A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.665A pdb=" N VAL B 121 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 133 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 189 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 134 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.605A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N MET B 535 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY B 517 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 516 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 306 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 470 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AA9, first strand: chain 'B' and resid 373 through 374 removed outlier: 4.104A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 433 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1935 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: 1.93 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1856 1.32 - 1.45: 2658 1.45 - 1.57: 6567 1.57 - 1.69: 12 1.69 - 1.81: 112 Bond restraints: 11205 Sorted by residual: bond pdb=" OA3 CDL A 607 " pdb=" PA1 CDL A 607 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.74e+00 bond pdb=" OB3 CDL A 607 " pdb=" PB2 CDL A 607 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.35e+00 bond pdb=" OB3 CDL B 801 " pdb=" PB2 CDL B 801 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.19e+00 bond pdb=" OA3 CDL B 801 " pdb=" PA1 CDL B 801 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.17e+00 bond pdb=" C51 CDL A 607 " pdb=" C52 CDL A 607 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.50e-02 4.44e+03 4.58e+00 ... (remaining 11200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 14647 1.75 - 3.49: 447 3.49 - 5.24: 68 5.24 - 6.99: 34 6.99 - 8.73: 8 Bond angle restraints: 15204 Sorted by residual: angle pdb=" CB LYS B 419 " pdb=" CG LYS B 419 " pdb=" CD LYS B 419 " ideal model delta sigma weight residual 111.30 120.03 -8.73 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C LYS B 102 " pdb=" N THR B 103 " pdb=" CA THR B 103 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C VAL A 376 " pdb=" CA VAL A 376 " pdb=" CB VAL A 376 " ideal model delta sigma weight residual 111.23 114.94 -3.71 1.01e+00 9.80e-01 1.35e+01 angle pdb=" N GLY B 452 " pdb=" CA GLY B 452 " pdb=" C GLY B 452 " ideal model delta sigma weight residual 110.95 116.91 -5.96 1.70e+00 3.46e-01 1.23e+01 angle pdb=" N GLY A 375 " pdb=" CA GLY A 375 " pdb=" C GLY A 375 " ideal model delta sigma weight residual 111.78 117.31 -5.53 1.69e+00 3.50e-01 1.07e+01 ... (remaining 15199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5931 17.95 - 35.90: 595 35.90 - 53.85: 129 53.85 - 71.80: 29 71.80 - 89.75: 11 Dihedral angle restraints: 6695 sinusoidal: 2589 harmonic: 4106 Sorted by residual: dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta harmonic sigma weight residual 180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1232 0.042 - 0.084: 427 0.084 - 0.126: 126 0.126 - 0.167: 21 0.167 - 0.209: 5 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR B 313 " pdb=" CA THR B 313 " pdb=" OG1 THR B 313 " pdb=" CG2 THR B 313 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA4 CDL B 801 " pdb=" CA3 CDL B 801 " pdb=" CA6 CDL B 801 " pdb=" OA6 CDL B 801 " both_signs ideal model delta sigma weight residual False -2.57 -2.38 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 1808 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 121 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B 122 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 262 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO A 263 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 75 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO C 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 3200 2.82 - 3.40: 12416 3.40 - 3.98: 21354 3.98 - 4.56: 30546 4.56 - 5.14: 44405 Nonbonded interactions: 111921 Sorted by model distance: nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP B 329 " pdb=" OG1 THR B 332 " model vdw 2.267 3.040 nonbonded pdb=" O GLN B 318 " pdb=" OG SER B 351 " model vdw 2.274 3.040 nonbonded pdb=" O LEU B 239 " pdb=" OG SER B 243 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR B 471 " pdb=" OD1 ASP B 473 " model vdw 2.298 3.040 ... (remaining 111916 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.520 Find NCS groups from input model: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.004 0.053 11205 Z= 0.197 Angle : 0.748 8.731 15204 Z= 0.386 Chirality : 0.047 0.209 1811 Planarity : 0.006 0.065 1909 Dihedral : 15.558 89.752 4057 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.20), residues: 1439 helix: 0.20 (0.16), residues: 843 sheet: -1.36 (0.74), residues: 56 loop : -2.07 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 293 TYR 0.023 0.002 TYR C 170 PHE 0.029 0.002 PHE A 260 TRP 0.006 0.001 TRP B 655 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (11205) covalent geometry : angle 0.74754 / 0.39 (15204) hydrogen bonds : bond 0.09815 / 6.24 ( 659) hydrogen bonds : angle 5.16638 / 3.80 ( 1935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.384 Fit side-chains REVERT: A 71 MET cc_start: 0.8244 (mmt) cc_final: 0.7738 (mmt) REVERT: A 130 MET cc_start: 0.8478 (ttp) cc_final: 0.8118 (ttm) REVERT: B 77 LEU cc_start: 0.7944 (tt) cc_final: 0.7736 (tt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0841 time to fit residues: 19.0776 Evaluate side-chains 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 482 ASN C 80 GLN C 154 GLN B 316 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114610 restraints weight = 14581.866| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.28 r_work: 0.3057 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11205 Z= 0.119 Angle : 0.521 7.249 15204 Z= 0.269 Chirality : 0.039 0.142 1811 Planarity : 0.004 0.053 1909 Dihedral : 10.458 59.812 1675 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.18 % Allowed : 6.87 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1439 helix: 1.06 (0.17), residues: 842 sheet: -1.21 (0.63), residues: 69 loop : -1.85 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 293 TYR 0.028 0.001 TYR A 381 PHE 0.011 0.001 PHE A 260 TRP 0.009 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11205) covalent geometry : angle 0.52149 / 0.27 (15204) hydrogen bonds : bond 0.03687 / 2.43 ( 659) hydrogen bonds : angle 4.30671 / 3.15 ( 1935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.401 Fit side-chains REVERT: A 130 MET cc_start: 0.9003 (ttp) cc_final: 0.8610 (ttm) REVERT: B 23 LYS cc_start: 0.7079 (mmtt) cc_final: 0.6031 (mttt) REVERT: B 673 ASP cc_start: 0.8658 (t70) cc_final: 0.8409 (t0) outliers start: 2 outliers final: 2 residues processed: 127 average time/residue: 0.0845 time to fit residues: 16.1683 Evaluate side-chains 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN B 474 ASN 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 = 0.139172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105992 restraints weight = 14919.453| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.33 r_work: 0.3003 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11205 Z= 0.132 Angle : 0.516 7.310 15204 Z= 0.263 Chirality : 0.040 0.143 1811 Planarity : 0.004 0.052 1909 Dihedral : 9.484 58.231 1675 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.53 % Allowed : 9.34 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1439 helix: 1.26 (0.17), residues: 853 sheet: -1.11 (0.64), residues: 69 loop : -1.71 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 293 TYR 0.027 0.001 TYR A 381 PHE 0.013 0.001 PHE A 354 TRP 0.008 0.001 TRP B 31 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11205) covalent geometry : angle 0.51636 / 0.26 (15204) hydrogen bonds : bond 0.03692 / 2.47 ( 659) hydrogen bonds : angle 4.22926 / 3.09 ( 1935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.372 Fit side-chains REVERT: A 130 MET cc_start: 0.9045 (ttp) cc_final: 0.8801 (ttm) REVERT: B 23 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6053 (mttt) outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.0783 time to fit residues: 15.0644 Evaluate side-chains 116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 136 optimal weight: 0.1980 chunk 81 optimal weight: 0.0470 chunk 103 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 ASN B 217 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.099633 restraints weight = 15086.949| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.59 r_work: 0.3020 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11205 Z= 0.115 Angle : 0.494 7.261 15204 Z= 0.253 Chirality : 0.039 0.137 1811 Planarity : 0.004 0.052 1909 Dihedral : 9.019 59.876 1675 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.97 % Allowed : 11.01 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1439 helix: 1.50 (0.18), residues: 850 sheet: -0.98 (0.66), residues: 69 loop : -1.66 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.025 0.001 TYR A 381 PHE 0.010 0.001 PHE A 260 TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (11205) covalent geometry : angle 0.49442 / 0.25 (15204) hydrogen bonds : bond 0.03485 / 2.32 ( 659) hydrogen bonds : angle 4.13561 / 3.02 ( 1935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.317 Fit side-chains REVERT: A 130 MET cc_start: 0.9068 (ttp) cc_final: 0.8825 (ttm) REVERT: A 227 MET cc_start: 0.8794 (mmp) cc_final: 0.8320 (mmp) REVERT: B 25 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7563 (pp) REVERT: B 383 MET cc_start: 0.6035 (ttp) cc_final: 0.5337 (tmm) outliers start: 11 outliers final: 6 residues processed: 132 average time/residue: 0.0657 time to fit residues: 13.5323 Evaluate side-chains 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 119 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 GLN B 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103433 restraints weight = 14875.076| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.33 r_work: 0.2990 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11205 Z= 0.122 Angle : 0.502 7.259 15204 Z= 0.255 Chirality : 0.039 0.133 1811 Planarity : 0.004 0.052 1909 Dihedral : 8.780 59.871 1675 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.15 % Allowed : 12.07 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1439 helix: 1.54 (0.18), residues: 853 sheet: -0.82 (0.68), residues: 69 loop : -1.66 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.022 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11205) covalent geometry : angle 0.50165 / 0.25 (15204) hydrogen bonds : bond 0.03509 / 2.34 ( 659) hydrogen bonds : angle 4.12518 / 3.01 ( 1935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.277 Fit side-chains REVERT: A 130 MET cc_start: 0.9027 (ttp) cc_final: 0.8785 (ttm) REVERT: A 227 MET cc_start: 0.8766 (mmp) cc_final: 0.8426 (mmp) REVERT: A 413 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: B 25 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7616 (pp) REVERT: B 383 MET cc_start: 0.6047 (ttp) cc_final: 0.5373 (tmm) REVERT: B 535 MET cc_start: 0.7835 (mmm) cc_final: 0.7583 (mtp) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 0.0720 time to fit residues: 14.4862 Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 126 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 135 optimal weight: 0.0270 chunk 124 optimal weight: 0.0980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN C 154 GLN B 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.104951 restraints weight = 14923.957| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.32 r_work: 0.3024 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11205 Z= 0.121 Angle : 0.507 10.246 15204 Z= 0.256 Chirality : 0.039 0.133 1811 Planarity : 0.004 0.054 1909 Dihedral : 8.530 59.971 1675 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.06 % Allowed : 12.95 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1439 helix: 1.59 (0.18), residues: 853 sheet: -0.70 (0.70), residues: 69 loop : -1.63 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.023 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.008 0.001 TRP B 31 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (11205) covalent geometry : angle 0.50711 / 0.26 (15204) hydrogen bonds : bond 0.03497 / 2.32 ( 659) hydrogen bonds : angle 4.10684 / 3.01 ( 1935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.321 Fit side-chains REVERT: A 130 MET cc_start: 0.8994 (ttp) cc_final: 0.8732 (ttm) REVERT: A 227 MET cc_start: 0.8756 (mmp) cc_final: 0.8434 (mmp) REVERT: A 413 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: B 25 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7713 (pp) REVERT: B 383 MET cc_start: 0.5901 (ttp) cc_final: 0.5244 (tmm) REVERT: B 535 MET cc_start: 0.7861 (mmm) cc_final: 0.7219 (mtp) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.0758 time to fit residues: 14.8050 Evaluate side-chains 121 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097833 restraints weight = 15022.525| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.61 r_work: 0.2948 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11205 Z= 0.129 Angle : 0.519 8.277 15204 Z= 0.264 Chirality : 0.039 0.142 1811 Planarity : 0.004 0.055 1909 Dihedral : 8.371 59.734 1675 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.23 % Allowed : 13.04 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1439 helix: 1.60 (0.18), residues: 853 sheet: -0.75 (0.69), residues: 69 loop : -1.62 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.024 0.001 TYR A 381 PHE 0.009 0.001 PHE A 354 TRP 0.008 0.001 TRP B 31 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11205) covalent geometry : angle 0.51942 / 0.26 (15204) hydrogen bonds : bond 0.03548 / 2.37 ( 659) hydrogen bonds : angle 4.11874 / 3.01 ( 1935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.9066 (ttp) cc_final: 0.8809 (ttm) REVERT: A 227 MET cc_start: 0.8821 (mmp) cc_final: 0.8489 (mmp) REVERT: A 413 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: A 544 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8640 (mm) REVERT: B 25 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7584 (pp) REVERT: B 383 MET cc_start: 0.5952 (ttp) cc_final: 0.5306 (tmm) REVERT: B 431 LEU cc_start: 0.8135 (mm) cc_final: 0.7534 (tt) REVERT: B 535 MET cc_start: 0.7928 (mmm) cc_final: 0.7146 (mtp) outliers start: 14 outliers final: 9 residues processed: 128 average time/residue: 0.0777 time to fit residues: 15.3786 Evaluate side-chains 124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 135 optimal weight: 0.0040 chunk 136 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109425 restraints weight = 14768.215| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.28 r_work: 0.2993 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11205 Z= 0.118 Angle : 0.506 7.232 15204 Z= 0.259 Chirality : 0.039 0.141 1811 Planarity : 0.004 0.053 1909 Dihedral : 8.196 59.990 1675 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.32 % Allowed : 12.69 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1439 helix: 1.67 (0.18), residues: 848 sheet: -0.68 (0.70), residues: 69 loop : -1.54 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 293 TYR 0.023 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (11205) covalent geometry : angle 0.50620 / 0.26 (15204) hydrogen bonds : bond 0.03468 / 2.31 ( 659) hydrogen bonds : angle 4.07857 / 2.99 ( 1935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.8943 (ttp) cc_final: 0.8655 (ttm) REVERT: A 227 MET cc_start: 0.8726 (mmp) cc_final: 0.8395 (mmp) REVERT: A 413 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: B 25 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7583 (pp) REVERT: B 383 MET cc_start: 0.5958 (ttp) cc_final: 0.5284 (tmm) REVERT: B 431 LEU cc_start: 0.8073 (mm) cc_final: 0.7479 (tt) REVERT: B 535 MET cc_start: 0.7944 (mmm) cc_final: 0.7224 (mtp) outliers start: 15 outliers final: 10 residues processed: 130 average time/residue: 0.0820 time to fit residues: 16.2644 Evaluate side-chains 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 608 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 106 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110844 restraints weight = 14561.372| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.45 r_work: 0.3090 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11205 Z= 0.131 Angle : 0.523 10.017 15204 Z= 0.266 Chirality : 0.039 0.150 1811 Planarity : 0.004 0.054 1909 Dihedral : 8.156 58.810 1675 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.15 % Allowed : 13.13 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1439 helix: 1.62 (0.18), residues: 848 sheet: -1.05 (0.65), residues: 79 loop : -1.48 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 293 TYR 0.023 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.011 0.001 TRP B 186 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11205) covalent geometry : angle 0.52282 / 0.27 (15204) hydrogen bonds : bond 0.03537 / 2.36 ( 659) hydrogen bonds : angle 4.10713 / 3.00 ( 1935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.391 Fit side-chains REVERT: A 130 MET cc_start: 0.8956 (ttp) cc_final: 0.8664 (ttm) REVERT: A 227 MET cc_start: 0.8861 (mmp) cc_final: 0.8571 (mmp) REVERT: A 413 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: C 130 ASN cc_start: 0.8565 (p0) cc_final: 0.8308 (p0) REVERT: B 25 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7827 (pp) REVERT: B 383 MET cc_start: 0.6051 (ttp) cc_final: 0.5409 (tmm) REVERT: B 535 MET cc_start: 0.7974 (mmm) cc_final: 0.7411 (mtp) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.0779 time to fit residues: 14.5128 Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 608 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 6 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 107 optimal weight: 0.0970 chunk 120 optimal weight: 20.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109944 restraints weight = 14601.331| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.16 r_work: 0.3018 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11205 Z= 0.108 Angle : 0.510 8.352 15204 Z= 0.260 Chirality : 0.039 0.141 1811 Planarity : 0.004 0.054 1909 Dihedral : 7.948 57.769 1675 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.06 % Allowed : 13.22 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.22), residues: 1439 helix: 1.71 (0.18), residues: 848 sheet: -1.09 (0.65), residues: 79 loop : -1.45 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.023 0.001 TYR A 381 PHE 0.010 0.001 PHE A 527 TRP 0.006 0.001 TRP B 31 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11205) covalent geometry : angle 0.51016 / 0.26 (15204) hydrogen bonds : bond 0.03371 / 2.24 ( 659) hydrogen bonds : angle 4.03137 / 2.95 ( 1935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.419 Fit side-chains REVERT: A 130 MET cc_start: 0.8908 (ttp) cc_final: 0.8624 (ttm) REVERT: A 227 MET cc_start: 0.8674 (mmp) cc_final: 0.8438 (mmp) REVERT: A 413 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: B 25 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7582 (pp) REVERT: B 383 MET cc_start: 0.5940 (ttp) cc_final: 0.5281 (tmm) REVERT: B 431 LEU cc_start: 0.8017 (mm) cc_final: 0.7416 (tt) REVERT: B 535 MET cc_start: 0.7934 (mmm) cc_final: 0.7312 (mtp) outliers start: 12 outliers final: 9 residues processed: 126 average time/residue: 0.0835 time to fit residues: 15.9344 Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 608 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 107 optimal weight: 0.0270 chunk 126 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 ASN ** B 536 ASN ** 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 = 0.3700 r_free = 0.3700 target = 0.144432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112466 restraints weight = 14504.258| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.38 r_work: 0.3137 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11205 Z= 0.110 Angle : 0.509 8.381 15204 Z= 0.260 Chirality : 0.039 0.146 1811 Planarity : 0.004 0.054 1909 Dihedral : 7.810 58.359 1675 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.06 % Allowed : 13.39 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.22), residues: 1439 helix: 1.75 (0.18), residues: 849 sheet: -1.56 (0.64), residues: 69 loop : -1.37 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.023 0.001 TYR A 62 PHE 0.010 0.001 PHE A 527 TRP 0.006 0.001 TRP B 31 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11205) covalent geometry : angle 0.50871 / 0.26 (15204) hydrogen bonds : bond 0.03363 / 2.24 ( 659) hydrogen bonds : angle 4.03040 / 2.95 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.31 seconds wall clock time: 40 minutes 42.71 seconds (2442.71 seconds total)