Starting phenix.real_space_refine on Wed Mar 4 06:11:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrh_14914/03_2026/7zrh_14914.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrh_14914/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrh_14914/03_2026/7zrh_14914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrh_14914/03_2026/7zrh_14914.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrh_14914/03_2026/7zrh_14914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrh_14914/03_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-5986/lib/python3.9/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: 2.49, per 1000 atoms: 0.23 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: 0.75 Conformation dependent library (CDL) restraints added in 557.2 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: 0.35 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: 0.96 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: 5949 17.95 - 35.90: 601 35.90 - 53.85: 139 53.85 - 71.80: 35 71.80 - 89.75: 11 Dihedral angle restraints: 6735 sinusoidal: 2629 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 6732 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.280 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 15.889 89.752 4097 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 covalent geometry : bond 0.00403 (11205) covalent geometry : angle 0.74754 (15204) hydrogen bonds : bond 0.09815 ( 659) hydrogen bonds : angle 5.16638 ( 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 : 0.438 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: 0.0902 time to fit residues: 20.2888 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 : 0.398 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3711 r_free = 0.3711 target = 0.145695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114644 restraints weight = 14571.759| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.28 r_work: 0.3059 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11205 Z= 0.120 Angle : 0.523 7.263 15204 Z= 0.270 Chirality : 0.039 0.141 1811 Planarity : 0.004 0.053 1909 Dihedral : 11.441 59.831 1715 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 1.09 (0.17), residues: 836 sheet: -1.18 (0.63), residues: 69 loop : -1.88 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.029 0.001 TYR A 381 PHE 0.011 0.001 PHE A 260 TRP 0.008 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00264 (11205) covalent geometry : angle 0.52335 (15204) hydrogen bonds : bond 0.03716 ( 659) hydrogen bonds : angle 4.31133 ( 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 : 0.355 Fit side-chains REVERT: A 130 MET cc_start: 0.9003 (ttp) cc_final: 0.8605 (ttm) REVERT: B 23 LYS cc_start: 0.7097 (mmtt) cc_final: 0.6040 (mttt) REVERT: B 673 ASP cc_start: 0.8665 (t70) cc_final: 0.8412 (t0) outliers start: 2 outliers final: 2 residues processed: 127 average time/residue: 0.0910 time to fit residues: 17.2273 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 : 0.395 ------------------------------------------------------------------------------- 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: 9.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111343 restraints weight = 14693.458| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.31 r_work: 0.2981 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11205 Z= 0.148 Angle : 0.532 7.305 15204 Z= 0.271 Chirality : 0.040 0.145 1811 Planarity : 0.004 0.053 1909 Dihedral : 10.436 59.890 1715 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.53 % Allowed : 9.25 % Favored : 90.22 % 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: 0.06 (0.22), residues: 1439 helix: 1.19 (0.17), residues: 856 sheet: -1.09 (0.65), residues: 69 loop : -1.78 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.028 0.001 TYR A 381 PHE 0.015 0.001 PHE A 354 TRP 0.009 0.001 TRP B 31 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00344 (11205) covalent geometry : angle 0.53224 (15204) hydrogen bonds : bond 0.03840 ( 659) hydrogen bonds : angle 4.27878 ( 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 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.374 Fit side-chains REVERT: A 130 MET cc_start: 0.9018 (ttp) cc_final: 0.8777 (ttm) REVERT: B 23 LYS cc_start: 0.7204 (mmtt) cc_final: 0.6143 (mttt) outliers start: 6 outliers final: 4 residues processed: 127 average time/residue: 0.0877 time to fit residues: 16.7665 Evaluate side-chains 113 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 7.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN B 217 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099221 restraints weight = 15097.516| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.51 r_work: 0.2991 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1409 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 : 0.504 7.265 15204 Z= 0.257 Chirality : 0.039 0.137 1811 Planarity : 0.004 0.051 1909 Dihedral : 10.005 59.561 1715 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.06 % Allowed : 10.84 % Favored : 88.11 % 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: 0.29 (0.22), residues: 1439 helix: 1.37 (0.18), residues: 858 sheet: -0.98 (0.66), residues: 69 loop : -1.71 (0.25), residues: 512 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 0.010 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 covalent geometry : bond 0.00277 (11205) covalent geometry : angle 0.50422 (15204) hydrogen bonds : bond 0.03596 ( 659) hydrogen bonds : angle 4.19211 ( 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 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.369 Fit side-chains REVERT: A 130 MET cc_start: 0.9065 (ttp) cc_final: 0.8844 (ttm) REVERT: B 23 LYS cc_start: 0.7234 (mmtt) cc_final: 0.6087 (mttt) REVERT: B 25 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7518 (pp) REVERT: B 383 MET cc_start: 0.5981 (ttp) cc_final: 0.5327 (tmm) outliers start: 12 outliers final: 7 residues processed: 128 average time/residue: 0.0834 time to fit residues: 16.3070 Evaluate side-chains 119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 263 ILE 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: 0.7980 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN C 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103814 restraints weight = 14857.833| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.32 r_work: 0.3005 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1482 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= 0.123 Angle : 0.504 7.252 15204 Z= 0.257 Chirality : 0.039 0.133 1811 Planarity : 0.004 0.053 1909 Dihedral : 9.639 58.326 1715 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.97 % Allowed : 12.51 % Favored : 86.52 % 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: 0.41 (0.22), residues: 1439 helix: 1.49 (0.18), residues: 852 sheet: -0.82 (0.68), residues: 69 loop : -1.68 (0.25), residues: 518 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 0.010 0.001 PHE A 527 TRP 0.008 0.001 TRP B 31 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00281 (11205) covalent geometry : angle 0.50402 (15204) hydrogen bonds : bond 0.03580 ( 659) hydrogen bonds : angle 4.15970 ( 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 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.397 Fit side-chains REVERT: A 130 MET cc_start: 0.9034 (ttp) cc_final: 0.8807 (ttm) REVERT: B 25 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 383 MET cc_start: 0.5877 (ttp) cc_final: 0.5218 (tmm) outliers start: 11 outliers final: 9 residues processed: 128 average time/residue: 0.0785 time to fit residues: 15.5398 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 : 0.378 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.0010 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 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 = 0.3648 r_free = 0.3648 target = 0.140184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107612 restraints weight = 14743.821| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.32 r_work: 0.2922 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11205 Z= 0.164 Angle : 0.541 7.280 15204 Z= 0.275 Chirality : 0.040 0.142 1811 Planarity : 0.004 0.054 1909 Dihedral : 9.497 59.516 1715 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.97 % Allowed : 13.30 % 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: 0.35 (0.22), residues: 1439 helix: 1.36 (0.17), residues: 852 sheet: -0.74 (0.69), residues: 69 loop : -1.58 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.024 0.001 TYR A 381 PHE 0.014 0.001 PHE A 354 TRP 0.010 0.001 TRP B 31 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00387 (11205) covalent geometry : angle 0.54083 (15204) hydrogen bonds : bond 0.03852 ( 659) hydrogen bonds : angle 4.28716 ( 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 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.337 Fit side-chains REVERT: A 130 MET cc_start: 0.9019 (ttp) cc_final: 0.8787 (ttm) REVERT: A 413 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: B 25 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7790 (pp) REVERT: B 383 MET cc_start: 0.6059 (ttp) cc_final: 0.5423 (tmm) outliers start: 11 outliers final: 8 residues processed: 126 average time/residue: 0.0896 time to fit residues: 16.8217 Evaluate side-chains 124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097034 restraints weight = 14992.155| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.55 r_work: 0.2941 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1747 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= 0.121 Angle : 0.515 7.240 15204 Z= 0.263 Chirality : 0.039 0.132 1811 Planarity : 0.004 0.051 1909 Dihedral : 9.191 58.999 1715 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.32 % Allowed : 13.48 % Favored : 85.20 % 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: 0.54 (0.22), residues: 1439 helix: 1.56 (0.18), residues: 845 sheet: -0.78 (0.68), residues: 69 loop : -1.53 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.023 0.001 TYR A 381 PHE 0.010 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 covalent geometry : bond 0.00274 (11205) covalent geometry : angle 0.51530 (15204) hydrogen bonds : bond 0.03603 ( 659) hydrogen bonds : angle 4.17408 ( 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 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.9102 (ttp) cc_final: 0.8840 (ttm) REVERT: A 227 MET cc_start: 0.8841 (mmp) cc_final: 0.8383 (mmp) REVERT: A 413 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: C 130 ASN cc_start: 0.8568 (p0) cc_final: 0.8279 (p0) REVERT: B 25 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7520 (pp) REVERT: B 383 MET cc_start: 0.6004 (ttp) cc_final: 0.5360 (tmm) REVERT: B 431 LEU cc_start: 0.8070 (mm) cc_final: 0.7472 (tt) REVERT: B 535 MET cc_start: 0.7922 (mmm) cc_final: 0.7646 (mtp) outliers start: 15 outliers final: 10 residues processed: 132 average time/residue: 0.0831 time to fit residues: 16.8079 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 : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 124 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.131924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.095804 restraints weight = 15151.229| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.59 r_work: 0.2917 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11205 Z= 0.141 Angle : 0.535 9.853 15204 Z= 0.272 Chirality : 0.040 0.144 1811 Planarity : 0.004 0.052 1909 Dihedral : 9.119 59.928 1715 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.23 % Allowed : 14.19 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1439 helix: 1.52 (0.18), residues: 845 sheet: -1.10 (0.67), residues: 65 loop : -1.56 (0.25), residues: 529 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 0.010 0.001 PHE A 527 TRP 0.009 0.001 TRP B 31 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00327 (11205) covalent geometry : angle 0.53451 (15204) hydrogen bonds : bond 0.03660 ( 659) hydrogen bonds : angle 4.19608 ( 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 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.9089 (ttp) cc_final: 0.8821 (ttm) REVERT: A 413 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: C 130 ASN cc_start: 0.8604 (p0) cc_final: 0.8305 (p0) REVERT: B 25 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7539 (pp) REVERT: B 383 MET cc_start: 0.6089 (ttp) cc_final: 0.5445 (tmm) REVERT: B 535 MET cc_start: 0.8005 (mmm) cc_final: 0.7296 (mtp) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.0848 time to fit residues: 16.4898 Evaluate side-chains 125 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 124 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 106 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.139517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108332 restraints weight = 14645.405| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.25 r_work: 0.3002 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1859 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= 0.123 Angle : 0.521 8.635 15204 Z= 0.266 Chirality : 0.039 0.142 1811 Planarity : 0.004 0.053 1909 Dihedral : 8.952 59.993 1715 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.32 % Allowed : 14.01 % Favored : 84.67 % 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: 1.62 (0.18), residues: 841 sheet: -1.25 (0.70), residues: 59 loop : -1.49 (0.25), residues: 539 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 0.010 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 covalent geometry : bond 0.00279 (11205) covalent geometry : angle 0.52094 (15204) hydrogen bonds : bond 0.03557 ( 659) hydrogen bonds : angle 4.13414 ( 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 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.465 Fit side-chains REVERT: A 130 MET cc_start: 0.9000 (ttp) cc_final: 0.8711 (ttm) REVERT: A 227 MET cc_start: 0.8747 (mmp) cc_final: 0.8289 (mmp) REVERT: A 320 MET cc_start: 0.9324 (tpp) cc_final: 0.9040 (mmm) REVERT: A 413 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: B 25 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7590 (pp) REVERT: B 383 MET cc_start: 0.6052 (ttp) cc_final: 0.5394 (tmm) REVERT: B 535 MET cc_start: 0.7988 (mmm) cc_final: 0.7360 (mtp) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.0819 time to fit residues: 15.9772 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 : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 124 SER 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 6 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 3 optimal weight: 0.0770 chunk 49 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.141133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109601 restraints weight = 14698.818| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.20 r_work: 0.3016 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11205 Z= 0.112 Angle : 0.520 8.045 15204 Z= 0.265 Chirality : 0.039 0.146 1811 Planarity : 0.004 0.056 1909 Dihedral : 8.798 59.991 1715 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.06 % Allowed : 14.89 % Favored : 84.05 % 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: 0.64 (0.22), residues: 1439 helix: 1.66 (0.18), residues: 850 sheet: -1.62 (0.64), residues: 69 loop : -1.41 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.023 0.001 TYR A 381 PHE 0.011 0.001 PHE A 527 TRP 0.007 0.001 TRP B 186 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00248 (11205) covalent geometry : angle 0.51954 (15204) hydrogen bonds : bond 0.03448 ( 659) hydrogen bonds : angle 4.10548 ( 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 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.247 Fit side-chains REVERT: A 130 MET cc_start: 0.8980 (ttp) cc_final: 0.8699 (ttm) REVERT: A 227 MET cc_start: 0.8660 (mmp) cc_final: 0.8169 (mmp) REVERT: A 320 MET cc_start: 0.9314 (tpp) cc_final: 0.9030 (mmm) REVERT: A 413 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: C 130 ASN cc_start: 0.8507 (p0) cc_final: 0.8231 (p0) REVERT: B 25 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7461 (pp) REVERT: B 383 MET cc_start: 0.5997 (ttp) cc_final: 0.5340 (tmm) REVERT: B 431 LEU cc_start: 0.8044 (mm) cc_final: 0.7426 (tt) REVERT: B 535 MET cc_start: 0.7952 (mmm) cc_final: 0.7284 (mtp) outliers start: 12 outliers final: 9 residues processed: 126 average time/residue: 0.0857 time to fit residues: 16.4255 Evaluate side-chains 124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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: 0.7980 chunk 126 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.140960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109518 restraints weight = 14610.034| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.21 r_work: 0.2997 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11205 Z= 0.119 Angle : 0.518 7.233 15204 Z= 0.265 Chirality : 0.039 0.159 1811 Planarity : 0.004 0.054 1909 Dihedral : 8.712 59.494 1715 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.15 % Allowed : 14.54 % Favored : 84.32 % 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: 0.60 (0.22), residues: 1439 helix: 1.64 (0.18), residues: 852 sheet: -1.46 (0.62), residues: 75 loop : -1.49 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.023 0.001 TYR A 381 PHE 0.010 0.001 PHE A 527 TRP 0.007 0.001 TRP B 31 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00269 (11205) covalent geometry : angle 0.51827 (15204) hydrogen bonds : bond 0.03468 ( 659) hydrogen bonds : angle 4.10244 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.64 seconds wall clock time: 40 minutes 46.44 seconds (2446.44 seconds total)