Starting phenix.real_space_refine on Tue Jul 29 02:22:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r7x_4746/07_2025/6r7x_4746.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r7x_4746/07_2025/6r7x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6r7x_4746/07_2025/6r7x_4746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r7x_4746/07_2025/6r7x_4746.map" model { file = "/net/cci-nas-00/data/ceres_data/6r7x_4746/07_2025/6r7x_4746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r7x_4746/07_2025/6r7x_4746.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 4} 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: 317 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: 317 Unresolved non-hydrogen chiralities: 60 Time building chain proxies: 7.44, per 1000 atoms: 0.70 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.95 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: 3.35 Time building geometry restraints manager: 3.15 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 - 24.56: 6422 24.56 - 49.11: 340 49.11 - 73.67: 36 73.67 - 98.22: 4 98.22 - 122.78: 8 Dihedral angle restraints: 6810 sinusoidal: 3080 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=" C5 UMQ B 906 " pdb=" C1 UMQ B 906 " pdb=" O5 UMQ B 906 " pdb=" O1 UMQ B 906 " ideal model delta sinusoidal sigma weight residual 298.22 175.44 122.78 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 6807 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: 0.05 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.130 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 14.819 122.777 4402 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.001 TRP A 261 HIS 0.003 0.001 HIS B 347 PHE 0.016 0.002 PHE A 171 TYR 0.012 0.001 TYR A 377 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.13106 ( 618) hydrogen bonds : angle 6.26122 ( 1824) covalent geometry : bond 0.00503 (10872) covalent geometry : angle 0.78550 (14668) *********************** 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 : 1.139 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: 0.7693 (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: 0.2348 time to fit residues: 62.0634 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 : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 389 ASN A 411 ASN A 441 GLN A 504 GLN B 195 GLN B 389 ASN B 411 ASN B 504 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.097647 restraints weight = 12184.996| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.81 r_work: 0.2812 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10872 Z= 0.157 Angle : 0.527 8.867 14668 Z= 0.264 Chirality : 0.037 0.172 1676 Planarity : 0.004 0.046 1750 Dihedral : 10.123 77.840 2038 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 1.32 % Allowed : 7.64 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1254 helix: 0.32 (0.17), residues: 786 sheet: -0.54 (0.72), residues: 44 loop : -1.17 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.004 0.001 HIS B 174 PHE 0.024 0.001 PHE A 584 TYR 0.010 0.001 TYR A 217 ARG 0.003 0.000 ARG B 430 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 618) hydrogen bonds : angle 4.12253 ( 1824) covalent geometry : bond 0.00364 (10872) covalent geometry : angle 0.52688 (14668) *********************** 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 157 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.086 Fit side-chains REVERT: A 334 MET cc_start: 0.8255 (mmm) cc_final: 0.7994 (mmt) REVERT: A 339 MET cc_start: 0.8216 (ttm) cc_final: 0.7865 (ttm) REVERT: B 334 MET cc_start: 0.8304 (mmm) cc_final: 0.8034 (mmt) REVERT: B 339 MET cc_start: 0.8219 (ttm) cc_final: 0.7878 (ttm) REVERT: B 441 GLN cc_start: 0.7953 (mt0) cc_final: 0.7666 (mt0) outliers start: 14 outliers final: 8 residues processed: 150 average time/residue: 0.2319 time to fit residues: 49.1643 Evaluate side-chains 140 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 514 VAL 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 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 16 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS B 411 ASN B 459 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096627 restraints weight = 12328.753| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.81 r_work: 0.2802 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10872 Z= 0.166 Angle : 0.510 6.910 14668 Z= 0.256 Chirality : 0.037 0.164 1676 Planarity : 0.004 0.044 1750 Dihedral : 9.152 58.479 2038 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 1.79 % Allowed : 8.30 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1254 helix: 1.17 (0.18), residues: 782 sheet: -0.45 (0.73), residues: 44 loop : -0.88 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 342 HIS 0.004 0.001 HIS A 174 PHE 0.013 0.001 PHE A 584 TYR 0.009 0.001 TYR A 217 ARG 0.005 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 618) hydrogen bonds : angle 3.91728 ( 1824) covalent geometry : bond 0.00391 (10872) covalent geometry : angle 0.51024 (14668) *********************** 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: 19 poor density : 133 time to evaluate : 1.195 Fit side-chains REVERT: A 334 MET cc_start: 0.8243 (mmm) cc_final: 0.8003 (mmt) REVERT: A 339 MET cc_start: 0.8224 (ttm) cc_final: 0.7868 (ttm) REVERT: B 334 MET cc_start: 0.8261 (mmm) cc_final: 0.8022 (mmt) REVERT: B 339 MET cc_start: 0.8213 (ttm) cc_final: 0.7862 (ttm) outliers start: 19 outliers final: 15 residues processed: 146 average time/residue: 0.3165 time to fit residues: 66.4090 Evaluate side-chains 138 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 514 VAL 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 477 THR Chi-restraints excluded: chain B residue 480 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 107 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS B 67 GLN B 107 ASN 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 = 0.3406 r_free = 0.3406 target = 0.130806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.097272 restraints weight = 12337.575| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.85 r_work: 0.2819 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1786 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= 0.095 Angle : 0.441 5.748 14668 Z= 0.221 Chirality : 0.035 0.171 1676 Planarity : 0.003 0.043 1750 Dihedral : 8.276 57.648 2038 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 1.32 % Allowed : 10.38 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1254 helix: 1.75 (0.18), residues: 786 sheet: -0.30 (0.73), residues: 44 loop : -0.51 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 261 HIS 0.002 0.000 HIS B 174 PHE 0.011 0.001 PHE A 584 TYR 0.011 0.001 TYR B 211 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 618) hydrogen bonds : angle 3.68614 ( 1824) covalent geometry : bond 0.00209 (10872) covalent geometry : angle 0.44105 (14668) *********************** 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 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7078 (m-40) cc_final: 0.6300 (t0) REVERT: A 238 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8102 (mt-10) REVERT: A 334 MET cc_start: 0.8324 (mmm) cc_final: 0.8115 (mmt) REVERT: A 339 MET cc_start: 0.8286 (ttm) cc_final: 0.7943 (ttm) REVERT: B 107 ASN cc_start: 0.7074 (m-40) cc_final: 0.6317 (t0) REVERT: B 334 MET cc_start: 0.8332 (mmm) cc_final: 0.8123 (mmt) REVERT: B 339 MET cc_start: 0.8274 (ttm) cc_final: 0.7946 (ttm) outliers start: 14 outliers final: 7 residues processed: 141 average time/residue: 0.2125 time to fit residues: 43.6660 Evaluate side-chains 127 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 411 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS B 441 GLN B 459 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.094615 restraints weight = 12602.370| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.86 r_work: 0.2772 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1846 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= 0.136 Angle : 0.482 6.163 14668 Z= 0.242 Chirality : 0.037 0.181 1676 Planarity : 0.004 0.041 1750 Dihedral : 8.486 59.891 2038 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 1.70 % Allowed : 11.32 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1254 helix: 1.98 (0.18), residues: 782 sheet: 0.75 (0.87), residues: 34 loop : -0.45 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 342 HIS 0.003 0.001 HIS A 174 PHE 0.009 0.001 PHE A 584 TYR 0.020 0.001 TYR A 331 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 618) hydrogen bonds : angle 3.68877 ( 1824) covalent geometry : bond 0.00316 (10872) covalent geometry : angle 0.48204 (14668) *********************** 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 138 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7160 (m-40) cc_final: 0.6356 (t0) REVERT: A 334 MET cc_start: 0.8352 (mmm) cc_final: 0.8115 (mmt) REVERT: A 339 MET cc_start: 0.8313 (ttm) cc_final: 0.7957 (ttm) REVERT: B 107 ASN cc_start: 0.7185 (m-40) cc_final: 0.6390 (t0) REVERT: B 334 MET cc_start: 0.8342 (mmm) cc_final: 0.8107 (mmt) REVERT: B 339 MET cc_start: 0.8311 (ttm) cc_final: 0.7959 (ttm) outliers start: 18 outliers final: 12 residues processed: 133 average time/residue: 0.2227 time to fit residues: 43.9021 Evaluate side-chains 128 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 386 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 195 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS B 67 GLN B 195 GLN B 459 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.095680 restraints weight = 12575.016| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.84 r_work: 0.2792 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1967 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= 0.107 Angle : 0.456 6.285 14668 Z= 0.229 Chirality : 0.036 0.190 1676 Planarity : 0.003 0.042 1750 Dihedral : 8.260 58.661 2038 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 11.60 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.24), residues: 1254 helix: 2.21 (0.18), residues: 782 sheet: 1.00 (0.87), residues: 34 loop : -0.36 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 342 HIS 0.002 0.001 HIS A 174 PHE 0.008 0.001 PHE A 584 TYR 0.010 0.001 TYR B 211 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 618) hydrogen bonds : angle 3.61062 ( 1824) covalent geometry : bond 0.00239 (10872) covalent geometry : angle 0.45609 (14668) *********************** 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: 18 poor density : 125 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7076 (m-40) cc_final: 0.6330 (t0) REVERT: A 334 MET cc_start: 0.8337 (mmm) cc_final: 0.8103 (mmt) REVERT: A 339 MET cc_start: 0.8308 (ttm) cc_final: 0.7975 (ttm) REVERT: B 107 ASN cc_start: 0.7065 (m-40) cc_final: 0.6340 (t0) REVERT: B 334 MET cc_start: 0.8359 (mmm) cc_final: 0.8119 (mmt) REVERT: B 339 MET cc_start: 0.8302 (ttm) cc_final: 0.7978 (ttm) outliers start: 18 outliers final: 15 residues processed: 138 average time/residue: 0.2060 time to fit residues: 42.0613 Evaluate side-chains 134 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 44 LYS 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 477 THR Chi-restraints excluded: chain B residue 480 GLU 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 76 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 57 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 0.0060 chunk 99 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 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 = 0.3379 r_free = 0.3379 target = 0.128455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.094728 restraints weight = 12801.090| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.86 r_work: 0.2779 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1998 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= 0.119 Angle : 0.469 6.883 14668 Z= 0.236 Chirality : 0.036 0.217 1676 Planarity : 0.003 0.042 1750 Dihedral : 8.254 56.579 2038 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.24), residues: 1254 helix: 2.29 (0.18), residues: 784 sheet: 1.11 (0.86), residues: 34 loop : -0.26 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 342 HIS 0.003 0.001 HIS A 174 PHE 0.008 0.001 PHE A 584 TYR 0.021 0.001 TYR B 331 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 618) hydrogen bonds : angle 3.60041 ( 1824) covalent geometry : bond 0.00271 (10872) covalent geometry : angle 0.46927 (14668) *********************** 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 139 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7113 (m-40) cc_final: 0.6369 (t0) REVERT: A 334 MET cc_start: 0.8335 (mmm) cc_final: 0.8096 (mmt) REVERT: A 339 MET cc_start: 0.8325 (ttm) cc_final: 0.7985 (ttm) REVERT: B 107 ASN cc_start: 0.7116 (m-40) cc_final: 0.6380 (t0) REVERT: B 334 MET cc_start: 0.8350 (mmm) cc_final: 0.8113 (mmt) REVERT: B 339 MET cc_start: 0.8307 (ttm) cc_final: 0.7978 (ttm) outliers start: 18 outliers final: 16 residues processed: 133 average time/residue: 0.2019 time to fit residues: 40.2041 Evaluate side-chains 134 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 386 SER 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 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 90 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN B 459 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.094700 restraints weight = 12605.521| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.84 r_work: 0.2779 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2064 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= 0.121 Angle : 0.469 7.485 14668 Z= 0.235 Chirality : 0.036 0.216 1676 Planarity : 0.003 0.042 1750 Dihedral : 8.275 59.345 2038 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.60 % Allowed : 11.89 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.24), residues: 1254 helix: 2.38 (0.18), residues: 784 sheet: 1.19 (0.85), residues: 34 loop : -0.23 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 342 HIS 0.003 0.001 HIS A 174 PHE 0.008 0.001 PHE B 337 TYR 0.009 0.001 TYR B 211 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 618) hydrogen bonds : angle 3.59619 ( 1824) covalent geometry : bond 0.00278 (10872) covalent geometry : angle 0.46921 (14668) *********************** 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 138 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7097 (m-40) cc_final: 0.6386 (t0) REVERT: A 334 MET cc_start: 0.8341 (mmm) cc_final: 0.8103 (mmt) REVERT: A 339 MET cc_start: 0.8297 (ttm) cc_final: 0.7957 (ttm) REVERT: B 107 ASN cc_start: 0.7111 (m-40) cc_final: 0.6377 (t0) REVERT: B 334 MET cc_start: 0.8320 (mmm) cc_final: 0.8078 (mmt) REVERT: B 339 MET cc_start: 0.8285 (ttm) cc_final: 0.7950 (ttm) outliers start: 17 outliers final: 16 residues processed: 132 average time/residue: 0.2102 time to fit residues: 41.3805 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS 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 386 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 GLU 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 477 THR Chi-restraints excluded: chain B residue 480 GLU 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 96 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.126407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.092770 restraints weight = 12813.962| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.84 r_work: 0.2740 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10872 Z= 0.163 Angle : 0.512 8.184 14668 Z= 0.255 Chirality : 0.038 0.225 1676 Planarity : 0.003 0.042 1750 Dihedral : 8.423 57.277 2038 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.89 % Allowed : 11.98 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1254 helix: 2.29 (0.18), residues: 784 sheet: 1.11 (0.85), residues: 34 loop : -0.27 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 342 HIS 0.003 0.001 HIS A 174 PHE 0.012 0.001 PHE A 611 TYR 0.021 0.001 TYR B 331 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 618) hydrogen bonds : angle 3.67474 ( 1824) covalent geometry : bond 0.00385 (10872) covalent geometry : angle 0.51240 (14668) *********************** 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 139 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.111 Fit side-chains REVERT: A 107 ASN cc_start: 0.7205 (m-40) cc_final: 0.6391 (t0) REVERT: A 334 MET cc_start: 0.8354 (mmm) cc_final: 0.8119 (mmt) REVERT: A 339 MET cc_start: 0.8293 (ttm) cc_final: 0.7943 (ttm) REVERT: B 107 ASN cc_start: 0.7208 (m-40) cc_final: 0.6406 (t0) REVERT: B 334 MET cc_start: 0.8369 (mmm) cc_final: 0.8132 (mmt) REVERT: B 339 MET cc_start: 0.8272 (ttm) cc_final: 0.7934 (ttm) outliers start: 20 outliers final: 20 residues processed: 130 average time/residue: 0.2125 time to fit residues: 40.8150 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS 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 386 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3392 r_free = 0.3392 target = 0.129474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.096114 restraints weight = 12602.336| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.83 r_work: 0.2792 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10872 Z= 0.100 Angle : 0.460 8.524 14668 Z= 0.231 Chirality : 0.036 0.221 1676 Planarity : 0.003 0.043 1750 Dihedral : 7.839 57.706 2038 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.70 % Allowed : 12.26 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.24), residues: 1254 helix: 2.45 (0.18), residues: 792 sheet: 1.35 (0.86), residues: 34 loop : -0.27 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 342 HIS 0.002 0.001 HIS A 174 PHE 0.009 0.001 PHE B 611 TYR 0.010 0.001 TYR A 211 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 618) hydrogen bonds : angle 3.56141 ( 1824) covalent geometry : bond 0.00221 (10872) covalent geometry : angle 0.46005 (14668) ********************** 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: 18 poor density : 129 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7110 (m-40) cc_final: 0.6398 (t0) REVERT: A 334 MET cc_start: 0.8369 (mmm) cc_final: 0.8131 (mmt) REVERT: A 339 MET cc_start: 0.8283 (ttm) cc_final: 0.7951 (ttm) REVERT: B 107 ASN cc_start: 0.7061 (m-40) cc_final: 0.6372 (t0) REVERT: B 334 MET cc_start: 0.8365 (mmm) cc_final: 0.8131 (mmt) REVERT: B 339 MET cc_start: 0.8273 (ttm) cc_final: 0.7953 (ttm) outliers start: 18 outliers final: 17 residues processed: 141 average time/residue: 0.2125 time to fit residues: 44.3102 Evaluate side-chains 137 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS 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 524 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 44 LYS 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 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 93 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3375 r_free = 0.3375 target = 0.128111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094905 restraints weight = 12629.577| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.82 r_work: 0.2774 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2165 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= 0.125 Angle : 0.481 8.433 14668 Z= 0.240 Chirality : 0.037 0.225 1676 Planarity : 0.003 0.042 1750 Dihedral : 7.809 57.782 2038 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.70 % Allowed : 12.26 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.24), residues: 1254 helix: 2.43 (0.18), residues: 792 sheet: 1.32 (0.87), residues: 34 loop : -0.22 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 342 HIS 0.003 0.001 HIS A 174 PHE 0.010 0.001 PHE B 611 TYR 0.021 0.001 TYR A 331 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 618) hydrogen bonds : angle 3.56262 ( 1824) covalent geometry : bond 0.00289 (10872) covalent geometry : angle 0.48109 (14668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5533.60 seconds wall clock time: 96 minutes 14.30 seconds (5774.30 seconds total)