Starting phenix.real_space_refine on Fri Sep 11 18:24:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6r7x_4746/09_2026/6r7x_4746.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r7x_4746/09_2026/6r7x_4746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2026/6r7x_4746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2026/6r7x_4746.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2026/6r7x_4746.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2026/6r7x_4746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2026/6r7x_4746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2026/6r7x_4746.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Ca 6 9.91 5 P 2 5.49 5 S 54 5.16 5 C 7072 2.51 5 N 1644 2.21 5 O 1852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10630 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5060 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 23, 'TRANS': 605} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 5060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5060 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 23, 'TRANS': 605} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 255 Unusual residues: {' CA': 3, 'PC1': 1, 'UMQ': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 60 Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 255 Unusual residues: {' CA': 3, 'PC1': 1, 'UMQ': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 60 Time building chain proxies: 2.39, per 1000 atoms: 0.22 Number of scatterers: 10630 At special positions: 0 Unit cell: (106.038, 104.394, 100.284, 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) Ca 6 19.99 S 54 16.00 P 2 15.00 O 1852 8.00 N 1644 7.00 C 7072 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: 0.71 Conformation dependent library (CDL) restraints added in 288.3 milliseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 66.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 28 through 41 removed outlier: 3.808A pdb=" N ALA A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.554A pdb=" N GLU A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.772A pdb=" N PHE A 108 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 196 through 220 removed outlier: 8.137A pdb=" N GLU A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N THR A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.806A pdb=" N ASP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 273 removed outlier: 4.058A pdb=" N LYS A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 Processing helix chain 'A' and resid 317 through 350 Processing helix chain 'A' and resid 360 through 386 removed outlier: 3.941A pdb=" N ARG A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 422 removed outlier: 3.859A pdb=" N TYR A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER A 415 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 449 removed outlier: 3.737A pdb=" N SER A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.699A pdb=" N ALA A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.679A pdb=" N TYR A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 510 removed outlier: 3.952A pdb=" N LEU A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 539 removed outlier: 4.116A pdb=" N ALA A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 575 removed outlier: 3.863A pdb=" N VAL A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 613 removed outlier: 4.002A pdb=" N LEU A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 641 removed outlier: 3.580A pdb=" N SER A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.807A pdb=" N ALA B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 4.554A pdb=" N GLU B 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN B 67 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.773A pdb=" N PHE B 108 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 196 through 220 removed outlier: 8.137A pdb=" N GLU B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N THR B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 235 Proline residue: B 231 - end of helix Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.807A pdb=" N ASP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 273 removed outlier: 4.058A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'B' and resid 317 through 350 Processing helix chain 'B' and resid 360 through 386 removed outlier: 3.940A pdb=" N ARG B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 422 removed outlier: 3.859A pdb=" N TYR B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER B 415 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 449 removed outlier: 3.737A pdb=" N SER B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 469 removed outlier: 3.699A pdb=" N ALA B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.679A pdb=" N TYR B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 removed outlier: 3.952A pdb=" N LEU B 501 " --> pdb=" O ASP B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 539 removed outlier: 4.116A pdb=" N ALA B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 575 removed outlier: 3.863A pdb=" N VAL B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 613 removed outlier: 4.002A pdb=" N LEU B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 641 removed outlier: 3.580A pdb=" N SER B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.517A pdb=" N VAL A 20 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A 170 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU A 22 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 4.308A pdb=" N LYS A 155 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.517A pdb=" N VAL B 20 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL B 170 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU B 22 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 137 removed outlier: 4.308A pdb=" N LYS B 155 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 294 618 hydrogen bonds defined for protein. 1824 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: 1.36 Time building geometry restraints manager: 0.94 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: 1570 1.32 - 1.44: 3023 1.44 - 1.56: 6185 1.56 - 1.68: 4 1.68 - 1.81: 90 Bond restraints: 10872 Sorted by residual: bond pdb=" O13 PC1 B 905 " pdb=" P PC1 B 905 " ideal model delta sigma weight residual 1.652 1.594 0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" O13 PC1 A 704 " pdb=" P PC1 A 704 " ideal model delta sigma weight residual 1.652 1.595 0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" O11 PC1 B 905 " pdb=" P PC1 B 905 " ideal model delta sigma weight residual 1.642 1.595 0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" O11 PC1 A 704 " pdb=" P PC1 A 704 " ideal model delta sigma weight residual 1.642 1.596 0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C11 PC1 B 905 " pdb=" O13 PC1 B 905 " ideal model delta sigma weight residual 1.407 1.451 -0.044 2.00e-02 2.50e+03 4.89e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 13927 1.58 - 3.16: 611 3.16 - 4.74: 96 4.74 - 6.32: 20 6.32 - 7.90: 14 Bond angle restraints: 14668 Sorted by residual: angle pdb=" C PHE A 204 " pdb=" N GLY A 205 " pdb=" CA GLY A 205 " ideal model delta sigma weight residual 121.45 115.10 6.35 1.54e+00 4.22e-01 1.70e+01 angle pdb=" C PHE B 204 " pdb=" N GLY B 205 " pdb=" CA GLY B 205 " ideal model delta sigma weight residual 121.45 115.12 6.33 1.54e+00 4.22e-01 1.69e+01 angle pdb=" N VAL B 357 " pdb=" CA VAL B 357 " pdb=" C VAL B 357 " ideal model delta sigma weight residual 112.50 107.05 5.45 1.39e+00 5.18e-01 1.54e+01 angle pdb=" N VAL A 357 " pdb=" CA VAL A 357 " pdb=" C VAL A 357 " ideal model delta sigma weight residual 112.50 107.05 5.45 1.39e+00 5.18e-01 1.54e+01 angle pdb=" C PHE B 235 " pdb=" N VAL B 236 " pdb=" CA VAL B 236 " ideal model delta sigma weight residual 121.97 128.93 -6.96 1.80e+00 3.09e-01 1.49e+01 ... (remaining 14663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 5767 18.05 - 36.10: 525 36.10 - 54.15: 90 54.15 - 72.19: 10 72.19 - 90.24: 4 Dihedral angle restraints: 6396 sinusoidal: 2666 harmonic: 3730 Sorted by residual: dihedral pdb=" CA ASN B 349 " pdb=" C ASN B 349 " pdb=" N SER B 350 " pdb=" CA SER B 350 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ASN A 349 " pdb=" C ASN A 349 " pdb=" N SER A 350 " pdb=" CA SER A 350 " ideal model delta harmonic sigma weight residual 180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN A 531 " pdb=" C ASN A 531 " pdb=" N SER A 532 " pdb=" CA SER A 532 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1210 0.042 - 0.083: 370 0.083 - 0.125: 67 0.125 - 0.167: 17 0.167 - 0.208: 12 Chirality restraints: 1676 Sorted by residual: chirality pdb=" C2 UMQ B 908 " pdb=" C1 UMQ B 908 " pdb=" C3 UMQ B 908 " pdb=" O2 UMQ B 908 " both_signs ideal model delta sigma weight residual False -2.29 -2.50 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C2 UMQ A 707 " pdb=" C1 UMQ A 707 " pdb=" C3 UMQ A 707 " pdb=" O2 UMQ A 707 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C2 UMQ A 705 " pdb=" C1 UMQ A 705 " pdb=" C3 UMQ A 705 " pdb=" O2 UMQ A 705 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1673 not shown) Planarity restraints: 1750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 283 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO B 284 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 283 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 284 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 223 " 0.036 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 224 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " 0.030 5.00e-02 4.00e+02 ... (remaining 1747 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3022 2.81 - 3.33: 9089 3.33 - 3.86: 17165 3.86 - 4.38: 19310 4.38 - 4.90: 34461 Nonbonded interactions: 83047 Sorted by model distance: nonbonded pdb=" OE2 GLU A 500 " pdb="CA CA A 701 " model vdw 2.289 2.510 nonbonded pdb=" OE2 GLU B 500 " pdb="CA CA B 902 " model vdw 2.289 2.510 nonbonded pdb=" OH TYR A 211 " pdb=" OD2 ASP A 533 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR B 211 " pdb=" OD2 ASP B 533 " model vdw 2.311 3.040 nonbonded pdb=" OE2 GLU A 448 " pdb="CA CA A 702 " model vdw 2.311 2.510 ... (remaining 83042 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 641 or resid 702 through 703 or (resid 706 thro \ ugh 708 and (name CA or name CB or name CG or name CD or name CH or name C1' or \ name C2' or name C3' or name C4' or name C5' or name C6' or name CC or name CF o \ r name CI or name CJ or name CK or name CL or name O1 or name O1' or name O2' or \ name O3' or name O5' or name O6')) or (resid 709 through 711 and (name CA or na \ me CB or name CG or name CD or name CH or name CC or name CF or name CI or name \ CJ or name CK or name CL )) or (resid 712 through 713 and (name CB or name CG or \ name CD or name CH or name CC or name CF or name CI or name CJ or name CK or na \ me CL )) or (resid 714 and (name CA or name CB or name CG or name CD or name CH \ or name CC or name CF or name CI or name CJ or name CK or name CL or name O1'))) \ ) selection = (chain 'B' and (resid 13 through 641 or resid 902 through 903 or (resid 906 thro \ ugh 908 and (name CA or name CB or name CG or name CD or name CH or name C1' or \ name C2' or name C3' or name C4' or name C5' or name C6' or name CC or name CF o \ r name CI or name CJ or name CK or name CL or name O1 or name O1' or name O2' or \ name O3' or name O5' or name O6')) or (resid 909 through 911 and (name CA or na \ me CB or name CG or name CD or name CH or name CC or name CF or name CI or name \ CJ or name CK or name CL )) or (resid 912 through 913 and (name CB or name CG or \ name CD or name CH or name CC or name CF or name CI or name CJ or name CK or na \ me CL )) or resid 914)) } 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: 1.080 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: 9.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10872 Z= 0.237 Angle : 0.786 7.900 14668 Z= 0.422 Chirality : 0.045 0.208 1676 Planarity : 0.007 0.060 1750 Dihedral : 13.627 90.242 3988 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.39 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -3.00 (0.18), residues: 1254 helix: -1.92 (0.13), residues: 758 sheet: -0.83 (0.68), residues: 44 loop : -1.94 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 378 TYR 0.012 0.001 TYR A 377 PHE 0.016 0.002 PHE A 171 TRP 0.019 0.001 TRP A 261 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 (10872) covalent geometry : angle 0.78550 / 0.42 (14668) hydrogen bonds : bond 0.13106 / 8.42 ( 618) hydrogen bonds : angle 6.26122 / 4.32 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.372 Fit side-chains REVERT: A 36 LYS cc_start: 0.8317 (tttt) cc_final: 0.8080 (ttmm) REVERT: A 334 MET cc_start: 0.7935 (mmm) cc_final: 0.7694 (mmt) REVERT: A 339 MET cc_start: 0.7624 (ttm) cc_final: 0.7415 (ttm) REVERT: B 94 ASP cc_start: 0.8287 (p0) cc_final: 0.8075 (p0) REVERT: B 334 MET cc_start: 0.7951 (mmm) cc_final: 0.7692 (mmt) REVERT: B 339 MET cc_start: 0.7621 (ttm) cc_final: 0.7409 (ttm) REVERT: B 627 LEU cc_start: 0.8766 (tp) cc_final: 0.8352 (mp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0970 time to fit residues: 26.0966 Evaluate side-chains 128 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 389 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 504 GLN B 195 GLN B 389 ASN ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.128694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094615 restraints weight = 12426.326| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.82 r_work: 0.2765 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10872 Z= 0.239 Angle : 0.580 8.731 14668 Z= 0.296 Chirality : 0.038 0.124 1676 Planarity : 0.005 0.046 1750 Dihedral : 8.285 52.762 1624 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.91 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 7.36 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.22), residues: 1254 helix: 0.19 (0.17), residues: 782 sheet: -0.71 (0.68), residues: 44 loop : -1.18 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 430 TYR 0.012 0.001 TYR A 217 PHE 0.022 0.002 PHE A 584 TRP 0.015 0.001 TRP B 342 HIS 0.005 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (10872) covalent geometry : angle 0.58047 / 0.30 (14668) hydrogen bonds : bond 0.04566 / 3.02 ( 618) hydrogen bonds : angle 4.24216 / 2.92 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.347 Fit side-chains REVERT: A 334 MET cc_start: 0.8280 (mmm) cc_final: 0.8039 (mmt) REVERT: A 462 ARG cc_start: 0.8867 (mtp180) cc_final: 0.8614 (mtm180) REVERT: B 334 MET cc_start: 0.8288 (mmm) cc_final: 0.8023 (mmt) REVERT: B 441 GLN cc_start: 0.8059 (mt0) cc_final: 0.7799 (mt0) outliers start: 18 outliers final: 14 residues processed: 144 average time/residue: 0.0920 time to fit residues: 19.6056 Evaluate side-chains 137 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN A 441 GLN A 459 HIS B 107 ASN B 411 ASN B 459 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.131658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.098031 restraints weight = 12226.267| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.81 r_work: 0.2814 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10872 Z= 0.128 Angle : 0.468 5.949 14668 Z= 0.239 Chirality : 0.036 0.161 1676 Planarity : 0.004 0.045 1750 Dihedral : 7.688 51.965 1624 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.91 % Favored : 97.93 % Rotamer: Outliers : 1.89 % Allowed : 9.06 % Favored : 89.06 % 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: 0.62 (0.23), residues: 1254 helix: 1.21 (0.18), residues: 782 sheet: -0.58 (0.69), residues: 44 loop : -0.92 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 430 TYR 0.009 0.001 TYR A 211 PHE 0.014 0.001 PHE A 584 TRP 0.016 0.001 TRP A 261 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10872) covalent geometry : angle 0.46849 / 0.24 (14668) hydrogen bonds : bond 0.03781 / 2.51 ( 618) hydrogen bonds : angle 3.89534 / 2.69 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.429 Fit side-chains REVERT: A 334 MET cc_start: 0.8230 (mmm) cc_final: 0.8022 (mmt) REVERT: A 339 MET cc_start: 0.8220 (ttm) cc_final: 0.7865 (ttm) REVERT: A 462 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8598 (mtm180) REVERT: B 334 MET cc_start: 0.8204 (mmm) cc_final: 0.7999 (mmt) REVERT: B 339 MET cc_start: 0.8233 (ttm) cc_final: 0.7883 (ttm) outliers start: 20 outliers final: 16 residues processed: 143 average time/residue: 0.1028 time to fit residues: 20.9648 Evaluate side-chains 139 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 0.0070 chunk 80 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN A 107 ASN A 411 ASN A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 411 ASN B 441 GLN B 459 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.097029 restraints weight = 12628.237| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.88 r_work: 0.2790 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10872 Z= 0.110 Angle : 0.447 5.774 14668 Z= 0.228 Chirality : 0.036 0.169 1676 Planarity : 0.004 0.042 1750 Dihedral : 7.394 51.953 1624 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.83 % Favored : 98.01 % Rotamer: Outliers : 1.60 % Allowed : 10.66 % Favored : 87.74 % 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: 1.30 (0.24), residues: 1254 helix: 1.76 (0.18), residues: 778 sheet: 0.35 (0.82), residues: 34 loop : -0.71 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.020 0.001 TYR A 331 PHE 0.011 0.001 PHE A 584 TRP 0.015 0.001 TRP A 261 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10872) covalent geometry : angle 0.44656 / 0.23 (14668) hydrogen bonds : bond 0.03565 / 2.36 ( 618) hydrogen bonds : angle 3.70419 / 2.56 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7237 (m-40) cc_final: 0.6470 (t0) REVERT: A 334 MET cc_start: 0.8341 (mmm) cc_final: 0.8139 (mmt) REVERT: A 339 MET cc_start: 0.8315 (ttm) cc_final: 0.7963 (ttm) REVERT: A 462 ARG cc_start: 0.8915 (mtp180) cc_final: 0.8636 (mtm180) REVERT: B 107 ASN cc_start: 0.7211 (m-40) cc_final: 0.6367 (t0) REVERT: B 334 MET cc_start: 0.8337 (mmm) cc_final: 0.8133 (mmt) REVERT: B 339 MET cc_start: 0.8309 (ttm) cc_final: 0.7966 (ttm) outliers start: 17 outliers final: 10 residues processed: 141 average time/residue: 0.0960 time to fit residues: 19.8985 Evaluate side-chains 128 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 37 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 HIS A 389 ASN A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 389 ASN B 441 GLN B 459 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098759 restraints weight = 12444.718| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.86 r_work: 0.2836 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10872 Z= 0.084 Angle : 0.424 5.934 14668 Z= 0.218 Chirality : 0.035 0.179 1676 Planarity : 0.003 0.043 1750 Dihedral : 6.933 51.482 1624 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.07 % Favored : 97.77 % Rotamer: Outliers : 1.51 % Allowed : 11.32 % Favored : 87.17 % 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: 1.80 (0.24), residues: 1254 helix: 2.13 (0.18), residues: 782 sheet: 0.75 (0.85), residues: 34 loop : -0.48 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 98 TYR 0.012 0.001 TYR A 211 PHE 0.009 0.001 PHE A 584 TRP 0.015 0.001 TRP A 261 HIS 0.001 0.000 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.08 (10872) covalent geometry : angle 0.42422 / 0.22 (14668) hydrogen bonds : bond 0.03124 / 2.07 ( 618) hydrogen bonds : angle 3.52789 / 2.44 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.6994 (m-40) cc_final: 0.6281 (t0) REVERT: A 334 MET cc_start: 0.8344 (mmm) cc_final: 0.8120 (mmt) REVERT: A 339 MET cc_start: 0.8281 (ttm) cc_final: 0.7949 (ttm) REVERT: B 107 ASN cc_start: 0.6934 (m-40) cc_final: 0.6253 (t0) REVERT: B 334 MET cc_start: 0.8350 (mmm) cc_final: 0.8119 (mmt) REVERT: B 339 MET cc_start: 0.8261 (ttm) cc_final: 0.7935 (ttm) outliers start: 16 outliers final: 10 residues processed: 143 average time/residue: 0.0954 time to fit residues: 20.0304 Evaluate side-chains 128 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 0.0980 chunk 93 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN A 289 HIS A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 459 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.094629 restraints weight = 12730.721| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.87 r_work: 0.2768 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10872 Z= 0.134 Angle : 0.474 6.359 14668 Z= 0.240 Chirality : 0.037 0.192 1676 Planarity : 0.004 0.041 1750 Dihedral : 7.268 52.310 1624 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.60 % Allowed : 11.60 % Favored : 86.79 % 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: 1.84 (0.24), residues: 1254 helix: 2.10 (0.18), residues: 794 sheet: 0.78 (0.86), residues: 34 loop : -0.42 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.020 0.001 TYR B 331 PHE 0.009 0.001 PHE A 611 TRP 0.018 0.001 TRP B 342 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (10872) covalent geometry : angle 0.47433 / 0.24 (14668) hydrogen bonds : bond 0.03621 / 2.40 ( 618) hydrogen bonds : angle 3.58545 / 2.48 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7129 (m-40) cc_final: 0.6360 (t0) REVERT: A 334 MET cc_start: 0.8351 (mmm) cc_final: 0.8132 (mmt) REVERT: A 339 MET cc_start: 0.8300 (ttm) cc_final: 0.7953 (ttm) REVERT: B 107 ASN cc_start: 0.7111 (m-40) cc_final: 0.6369 (t0) REVERT: B 334 MET cc_start: 0.8372 (mmm) cc_final: 0.8147 (mmt) REVERT: B 339 MET cc_start: 0.8285 (ttm) cc_final: 0.7938 (ttm) outliers start: 17 outliers final: 15 residues processed: 138 average time/residue: 0.0900 time to fit residues: 18.5492 Evaluate side-chains 132 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 120 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 459 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.097840 restraints weight = 12611.048| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.86 r_work: 0.2825 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10872 Z= 0.089 Angle : 0.431 7.107 14668 Z= 0.218 Chirality : 0.035 0.204 1676 Planarity : 0.003 0.042 1750 Dihedral : 6.912 51.747 1624 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.70 % Allowed : 11.70 % Favored : 86.60 % 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: 2.26 (0.24), residues: 1254 helix: 2.46 (0.18), residues: 782 sheet: 1.10 (0.83), residues: 34 loop : -0.24 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.010 0.001 TYR B 211 PHE 0.008 0.001 PHE A 584 TRP 0.018 0.001 TRP B 342 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (10872) covalent geometry : angle 0.43051 / 0.22 (14668) hydrogen bonds : bond 0.03179 / 2.11 ( 618) hydrogen bonds : angle 3.48600 / 2.42 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.6949 (m-40) cc_final: 0.6309 (t0) REVERT: A 334 MET cc_start: 0.8358 (mmm) cc_final: 0.8130 (mmt) REVERT: A 339 MET cc_start: 0.8304 (ttm) cc_final: 0.7959 (ttm) REVERT: B 107 ASN cc_start: 0.6943 (m-40) cc_final: 0.6313 (t0) REVERT: B 334 MET cc_start: 0.8346 (mmm) cc_final: 0.8117 (mmt) REVERT: B 339 MET cc_start: 0.8289 (ttm) cc_final: 0.7985 (ttm) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.0891 time to fit residues: 19.2795 Evaluate side-chains 137 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.125702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.091988 restraints weight = 12781.514| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.86 r_work: 0.2727 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10872 Z= 0.194 Angle : 0.530 7.401 14668 Z= 0.264 Chirality : 0.039 0.220 1676 Planarity : 0.004 0.040 1750 Dihedral : 7.838 52.962 1624 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.79 % Allowed : 12.26 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1254 helix: 2.06 (0.18), residues: 796 sheet: 0.93 (0.85), residues: 34 loop : -0.37 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.020 0.001 TYR B 331 PHE 0.011 0.001 PHE A 611 TRP 0.018 0.001 TRP B 342 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (10872) covalent geometry : angle 0.52989 / 0.26 (14668) hydrogen bonds : bond 0.04065 / 2.69 ( 618) hydrogen bonds : angle 3.65288 / 2.52 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.496 Fit side-chains REVERT: A 107 ASN cc_start: 0.7277 (m-40) cc_final: 0.6530 (t0) REVERT: A 334 MET cc_start: 0.8406 (mmm) cc_final: 0.8179 (mmt) REVERT: A 339 MET cc_start: 0.8324 (ttm) cc_final: 0.7968 (ttm) REVERT: A 462 ARG cc_start: 0.8905 (mtp180) cc_final: 0.8682 (mtm180) REVERT: B 107 ASN cc_start: 0.7261 (m-40) cc_final: 0.6522 (t0) REVERT: B 334 MET cc_start: 0.8392 (mmm) cc_final: 0.8170 (mmt) REVERT: B 339 MET cc_start: 0.8306 (ttm) cc_final: 0.7952 (ttm) outliers start: 19 outliers final: 17 residues processed: 133 average time/residue: 0.0890 time to fit residues: 17.7752 Evaluate side-chains 133 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 HIS B 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.094916 restraints weight = 12662.582| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.86 r_work: 0.2776 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10872 Z= 0.118 Angle : 0.468 8.157 14668 Z= 0.235 Chirality : 0.036 0.220 1676 Planarity : 0.003 0.043 1750 Dihedral : 7.432 52.706 1624 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.60 % Allowed : 13.02 % Favored : 85.38 % 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: 2.03 (0.24), residues: 1254 helix: 2.23 (0.18), residues: 796 sheet: 1.21 (0.85), residues: 34 loop : -0.36 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.008 0.001 TYR A 211 PHE 0.009 0.001 PHE A 611 TRP 0.019 0.001 TRP B 342 HIS 0.002 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10872) covalent geometry : angle 0.46834 / 0.23 (14668) hydrogen bonds : bond 0.03518 / 2.33 ( 618) hydrogen bonds : angle 3.56180 / 2.46 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.405 Fit side-chains REVERT: A 107 ASN cc_start: 0.7200 (m-40) cc_final: 0.6413 (t0) REVERT: A 334 MET cc_start: 0.8355 (mmm) cc_final: 0.8149 (mmt) REVERT: A 339 MET cc_start: 0.8294 (ttm) cc_final: 0.7949 (ttm) REVERT: A 462 ARG cc_start: 0.8894 (mtp180) cc_final: 0.8601 (mtm180) REVERT: B 107 ASN cc_start: 0.7184 (m-40) cc_final: 0.6418 (t0) REVERT: B 334 MET cc_start: 0.8337 (mmm) cc_final: 0.8134 (mmt) REVERT: B 339 MET cc_start: 0.8293 (ttm) cc_final: 0.7955 (ttm) outliers start: 17 outliers final: 17 residues processed: 136 average time/residue: 0.0891 time to fit residues: 18.2494 Evaluate side-chains 141 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 0.0010 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS B 67 GLN B 459 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.094528 restraints weight = 12640.129| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.84 r_work: 0.2771 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10872 Z= 0.128 Angle : 0.489 8.592 14668 Z= 0.243 Chirality : 0.037 0.226 1676 Planarity : 0.003 0.042 1750 Dihedral : 7.453 53.151 1624 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.79 % Allowed : 12.83 % Favored : 85.38 % 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: 2.01 (0.24), residues: 1254 helix: 2.18 (0.18), residues: 804 sheet: 1.23 (0.84), residues: 34 loop : -0.34 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.020 0.001 TYR B 331 PHE 0.010 0.001 PHE A 611 TRP 0.019 0.001 TRP B 342 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10872) covalent geometry : angle 0.48869 / 0.24 (14668) hydrogen bonds : bond 0.03594 / 2.38 ( 618) hydrogen bonds : angle 3.55581 / 2.46 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.415 Fit side-chains REVERT: A 107 ASN cc_start: 0.7169 (m-40) cc_final: 0.6411 (t0) REVERT: A 339 MET cc_start: 0.8297 (ttm) cc_final: 0.7945 (ttm) REVERT: B 107 ASN cc_start: 0.7157 (m-40) cc_final: 0.6411 (t0) REVERT: B 339 MET cc_start: 0.8285 (ttm) cc_final: 0.7942 (ttm) outliers start: 19 outliers final: 17 residues processed: 140 average time/residue: 0.0894 time to fit residues: 18.6371 Evaluate side-chains 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 HIS B 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.096519 restraints weight = 12625.744| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.85 r_work: 0.2803 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10872 Z= 0.102 Angle : 0.461 8.273 14668 Z= 0.230 Chirality : 0.036 0.225 1676 Planarity : 0.003 0.043 1750 Dihedral : 7.180 53.191 1624 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.98 % Allowed : 12.64 % Favored : 85.38 % 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: 2.17 (0.24), residues: 1254 helix: 2.29 (0.18), residues: 808 sheet: 1.41 (0.85), residues: 34 loop : -0.28 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.010 0.001 TYR A 211 PHE 0.009 0.001 PHE A 611 TRP 0.020 0.001 TRP B 342 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (10872) covalent geometry : angle 0.46144 / 0.23 (14668) hydrogen bonds : bond 0.03346 / 2.22 ( 618) hydrogen bonds : angle 3.49065 / 2.41 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2391.03 seconds wall clock time: 41 minutes 51.14 seconds (2511.14 seconds total)