Starting phenix.real_space_refine on Wed Sep 17 19:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r7x_4746/09_2025/6r7x_4746.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r7x_4746/09_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_4746/09_2025/6r7x_4746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2025/6r7x_4746.map" model { file = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2025/6r7x_4746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r7x_4746/09_2025/6r7x_4746.cif" } 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-2.0-5805/lib/python3.9/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: 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: 3.17, per 1000 atoms: 0.30 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: 1.19 Conformation dependent library (CDL) restraints added in 408.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.25 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: 1.62 Time building geometry restraints manager: 1.49 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: 0.02 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: 0.890 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00503 (10872) covalent geometry : angle 0.78550 (14668) hydrogen bonds : bond 0.13106 ( 618) hydrogen bonds : angle 6.26122 ( 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 : 0.376 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: 0.1024 time to fit residues: 27.2284 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 : 0.393 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.094736 restraints weight = 12424.348| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.82 r_work: 0.2767 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10872 Z= 0.241 Angle : 0.597 8.606 14668 Z= 0.300 Chirality : 0.039 0.141 1676 Planarity : 0.005 0.047 1750 Dihedral : 10.683 82.278 2038 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 1.98 % Allowed : 7.08 % 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 aren not related in a simple way. whole: -0.62 (0.22), residues: 1254 helix: 0.12 (0.17), residues: 782 sheet: -0.70 (0.68), residues: 44 loop : -1.20 (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 0.021 0.001 PHE A 584 TRP 0.015 0.001 TRP B 342 HIS 0.005 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00570 (10872) covalent geometry : angle 0.59673 (14668) hydrogen bonds : bond 0.04595 ( 618) hydrogen bonds : angle 4.27925 ( 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 155 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.368 Fit side-chains REVERT: A 334 MET cc_start: 0.8286 (mmm) cc_final: 0.8015 (mmt) REVERT: A 462 ARG cc_start: 0.8873 (mtp180) cc_final: 0.8621 (mtm180) REVERT: B 334 MET cc_start: 0.8296 (mmm) cc_final: 0.8028 (mmt) REVERT: B 441 GLN cc_start: 0.8044 (mt0) cc_final: 0.7814 (mt0) outliers start: 21 outliers final: 14 residues processed: 148 average time/residue: 0.0989 time to fit residues: 21.0218 Evaluate side-chains 139 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 10.0000 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 A 459 HIS B 411 ASN B 459 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.097312 restraints weight = 12256.841| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.81 r_work: 0.2806 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1544 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= 0.146 Angle : 0.493 6.401 14668 Z= 0.248 Chirality : 0.037 0.164 1676 Planarity : 0.004 0.045 1750 Dihedral : 9.151 58.519 2038 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.91 % Favored : 97.93 % Rotamer: Outliers : 1.89 % Allowed : 9.25 % Favored : 88.87 % 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 aren not related in a simple way. whole: 0.57 (0.23), residues: 1254 helix: 1.16 (0.18), residues: 782 sheet: -0.62 (0.69), residues: 44 loop : -0.90 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 430 TYR 0.009 0.001 TYR B 308 PHE 0.015 0.001 PHE A 584 TRP 0.016 0.001 TRP B 261 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00340 (10872) covalent geometry : angle 0.49258 (14668) hydrogen bonds : bond 0.03883 ( 618) hydrogen bonds : angle 3.92004 ( 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 151 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.405 Fit side-chains REVERT: A 334 MET cc_start: 0.8232 (mmm) cc_final: 0.8020 (mmt) REVERT: A 339 MET cc_start: 0.8229 (ttm) cc_final: 0.7878 (ttm) REVERT: A 462 ARG cc_start: 0.8845 (mtp180) cc_final: 0.8594 (mtm180) REVERT: B 334 MET cc_start: 0.8210 (mmm) cc_final: 0.8004 (mmt) REVERT: B 339 MET cc_start: 0.8238 (ttm) cc_final: 0.7889 (ttm) outliers start: 20 outliers final: 17 residues processed: 142 average time/residue: 0.1082 time to fit residues: 21.6883 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 365 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: 8.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 411 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.096730 restraints weight = 12556.655| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.87 r_work: 0.2813 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1752 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 : 0.442 5.758 14668 Z= 0.224 Chirality : 0.035 0.170 1676 Planarity : 0.004 0.043 1750 Dihedral : 8.365 56.325 2038 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 1.51 % Allowed : 10.38 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.24), residues: 1254 helix: 1.75 (0.18), residues: 782 sheet: 0.44 (0.83), residues: 34 loop : -0.67 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 98 TYR 0.012 0.001 TYR B 152 PHE 0.011 0.001 PHE A 584 TRP 0.016 0.001 TRP B 261 HIS 0.002 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00205 (10872) covalent geometry : angle 0.44236 (14668) hydrogen bonds : bond 0.03372 ( 618) hydrogen bonds : angle 3.68177 ( 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 150 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7105 (m-40) cc_final: 0.6330 (t0) REVERT: A 334 MET cc_start: 0.8330 (mmm) cc_final: 0.8129 (mmt) REVERT: A 339 MET cc_start: 0.8274 (ttm) cc_final: 0.7931 (ttm) REVERT: A 462 ARG cc_start: 0.8899 (mtp180) cc_final: 0.8597 (mtm180) REVERT: B 107 ASN cc_start: 0.7134 (m-40) cc_final: 0.6319 (t0) REVERT: B 334 MET cc_start: 0.8329 (mmm) cc_final: 0.8128 (mmt) REVERT: B 339 MET cc_start: 0.8281 (ttm) cc_final: 0.7946 (ttm) outliers start: 16 outliers final: 10 residues processed: 144 average time/residue: 0.0931 time to fit residues: 19.6584 Evaluate side-chains 132 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 A residue 524 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 365 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 chunk 84 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 106 optimal weight: 0.0970 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 389 ASN A 459 HIS B 289 HIS B 389 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 = 0.3421 r_free = 0.3421 target = 0.132332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.099161 restraints weight = 12436.185| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.84 r_work: 0.2838 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1945 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= 0.086 Angle : 0.435 5.774 14668 Z= 0.220 Chirality : 0.035 0.178 1676 Planarity : 0.003 0.043 1750 Dihedral : 8.046 59.620 2038 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.07 % Favored : 97.77 % Rotamer: Outliers : 1.23 % Allowed : 11.23 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.24), residues: 1254 helix: 2.09 (0.18), residues: 786 sheet: 0.80 (0.85), residues: 34 loop : -0.45 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 98 TYR 0.021 0.001 TYR B 331 PHE 0.009 0.001 PHE A 584 TRP 0.015 0.001 TRP B 342 HIS 0.002 0.000 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00178 (10872) covalent geometry : angle 0.43508 (14668) hydrogen bonds : bond 0.03127 ( 618) hydrogen bonds : angle 3.52902 ( 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 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.6988 (m-40) cc_final: 0.6285 (t0) REVERT: A 334 MET cc_start: 0.8332 (mmm) cc_final: 0.8107 (mmt) REVERT: A 339 MET cc_start: 0.8268 (ttm) cc_final: 0.7932 (ttm) REVERT: B 107 ASN cc_start: 0.6997 (m-40) cc_final: 0.6317 (t0) REVERT: B 334 MET cc_start: 0.8381 (mmm) cc_final: 0.8151 (mmt) REVERT: B 339 MET cc_start: 0.8266 (ttm) cc_final: 0.7958 (ttm) outliers start: 13 outliers final: 10 residues processed: 143 average time/residue: 0.0992 time to fit residues: 20.6900 Evaluate side-chains 132 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 A residue 524 LEU Chi-restraints excluded: chain B residue 44 LYS 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 524 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 289 HIS A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 441 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 = 0.3370 r_free = 0.3370 target = 0.127724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.094060 restraints weight = 12752.501| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.87 r_work: 0.2765 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10872 Z= 0.151 Angle : 0.497 6.507 14668 Z= 0.249 Chirality : 0.037 0.197 1676 Planarity : 0.003 0.041 1750 Dihedral : 8.373 58.153 2038 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.70 % Allowed : 11.13 % 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 aren not related in a simple way. whole: 1.77 (0.24), residues: 1254 helix: 2.04 (0.18), residues: 794 sheet: 0.76 (0.84), residues: 34 loop : -0.45 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.009 0.001 TYR A 203 PHE 0.010 0.001 PHE A 611 TRP 0.018 0.001 TRP A 342 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00353 (10872) covalent geometry : angle 0.49688 (14668) hydrogen bonds : bond 0.03713 ( 618) hydrogen bonds : angle 3.61203 ( 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 144 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7123 (m-40) cc_final: 0.6359 (t0) REVERT: A 334 MET cc_start: 0.8378 (mmm) cc_final: 0.8148 (mmt) REVERT: A 339 MET cc_start: 0.8311 (ttm) cc_final: 0.7960 (ttm) REVERT: A 462 ARG cc_start: 0.8911 (mtp180) cc_final: 0.8652 (mtm180) REVERT: B 107 ASN cc_start: 0.7132 (m-40) cc_final: 0.6384 (t0) REVERT: B 334 MET cc_start: 0.8369 (mmm) cc_final: 0.8125 (mmt) REVERT: B 339 MET cc_start: 0.8315 (ttm) cc_final: 0.7972 (ttm) REVERT: B 480 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8262 (pm20) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.0938 time to fit residues: 19.4394 Evaluate side-chains 133 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 441 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 = 0.3388 r_free = 0.3388 target = 0.129216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.095772 restraints weight = 12617.389| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.84 r_work: 0.2786 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2034 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 : 0.458 7.045 14668 Z= 0.229 Chirality : 0.036 0.202 1676 Planarity : 0.003 0.043 1750 Dihedral : 8.152 57.379 2038 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.51 % Allowed : 11.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.24), residues: 1254 helix: 2.33 (0.18), residues: 784 sheet: 0.99 (0.83), residues: 34 loop : -0.26 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.009 0.001 TYR B 211 PHE 0.009 0.001 PHE A 611 TRP 0.017 0.001 TRP B 342 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00242 (10872) covalent geometry : angle 0.45823 (14668) hydrogen bonds : bond 0.03394 ( 618) hydrogen bonds : angle 3.54128 ( 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 146 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7118 (m-40) cc_final: 0.6383 (t0) REVERT: A 334 MET cc_start: 0.8343 (mmm) cc_final: 0.8109 (mmt) REVERT: A 339 MET cc_start: 0.8298 (ttm) cc_final: 0.7967 (ttm) REVERT: A 462 ARG cc_start: 0.8950 (mtp180) cc_final: 0.8667 (mtm180) REVERT: B 107 ASN cc_start: 0.7097 (m-40) cc_final: 0.6398 (t0) REVERT: B 334 MET cc_start: 0.8315 (mmm) cc_final: 0.8077 (mmt) REVERT: B 339 MET cc_start: 0.8297 (ttm) cc_final: 0.7999 (ttm) outliers start: 16 outliers final: 13 residues processed: 140 average time/residue: 0.0866 time to fit residues: 18.2520 Evaluate side-chains 137 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 524 LEU Chi-restraints excluded: chain A residue 549 SER 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 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: 5.9990 chunk 1 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 390 HIS A 459 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 HIS ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.091410 restraints weight = 12812.303| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.84 r_work: 0.2720 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10872 Z= 0.208 Angle : 0.548 7.671 14668 Z= 0.272 Chirality : 0.039 0.222 1676 Planarity : 0.004 0.041 1750 Dihedral : 8.864 59.793 2038 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.24), residues: 1254 helix: 2.02 (0.18), residues: 792 sheet: 0.83 (0.85), residues: 34 loop : -0.46 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.020 0.001 TYR B 331 PHE 0.011 0.001 PHE B 611 TRP 0.017 0.001 TRP B 342 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00496 (10872) covalent geometry : angle 0.54756 (14668) hydrogen bonds : bond 0.04123 ( 618) hydrogen bonds : angle 3.71857 ( 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 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.319 Fit side-chains REVERT: A 107 ASN cc_start: 0.7361 (m-40) cc_final: 0.6601 (t0) REVERT: A 334 MET cc_start: 0.8386 (mmm) cc_final: 0.8154 (mmt) REVERT: A 339 MET cc_start: 0.8322 (ttm) cc_final: 0.7969 (ttm) REVERT: A 462 ARG cc_start: 0.8952 (mtp180) cc_final: 0.8729 (mtm180) REVERT: B 107 ASN cc_start: 0.7323 (m-40) cc_final: 0.6567 (t0) REVERT: B 334 MET cc_start: 0.8358 (mmm) cc_final: 0.8129 (mmt) REVERT: B 339 MET cc_start: 0.8314 (ttm) cc_final: 0.7974 (ttm) outliers start: 18 outliers final: 16 residues processed: 136 average time/residue: 0.0934 time to fit residues: 18.9832 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 : 0.407 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 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 459 HIS B 441 GLN B 459 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.095897 restraints weight = 12571.083| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.83 r_work: 0.2790 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10872 Z= 0.101 Angle : 0.464 8.060 14668 Z= 0.231 Chirality : 0.036 0.218 1676 Planarity : 0.003 0.043 1750 Dihedral : 8.068 57.330 2038 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 12.92 % 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 aren not related in a simple way. whole: 2.02 (0.24), residues: 1254 helix: 2.22 (0.18), residues: 800 sheet: 1.24 (0.85), residues: 34 loop : -0.38 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.009 0.001 TYR A 211 PHE 0.009 0.001 PHE B 611 TRP 0.019 0.001 TRP B 342 HIS 0.002 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00223 (10872) covalent geometry : angle 0.46385 (14668) hydrogen bonds : bond 0.03372 ( 618) hydrogen bonds : angle 3.57739 ( 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 153 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7140 (m-40) cc_final: 0.6400 (t0) REVERT: A 334 MET cc_start: 0.8333 (mmm) cc_final: 0.8126 (mmt) REVERT: A 339 MET cc_start: 0.8305 (ttm) cc_final: 0.7971 (ttm) REVERT: A 425 ASP cc_start: 0.8287 (p0) cc_final: 0.8026 (p0) REVERT: A 462 ARG cc_start: 0.8942 (mtp180) cc_final: 0.8660 (mtm180) REVERT: B 107 ASN cc_start: 0.7155 (m-40) cc_final: 0.6442 (t0) REVERT: B 339 MET cc_start: 0.8303 (ttm) cc_final: 0.7975 (ttm) REVERT: B 425 ASP cc_start: 0.8274 (p0) cc_final: 0.8022 (p0) outliers start: 18 outliers final: 17 residues processed: 146 average time/residue: 0.0909 time to fit residues: 19.8735 Evaluate side-chains 146 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.0030 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS B 67 GLN B 441 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 = 0.3383 r_free = 0.3383 target = 0.128799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.095667 restraints weight = 12530.360| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.82 r_work: 0.2784 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2180 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= 0.108 Angle : 0.479 8.576 14668 Z= 0.236 Chirality : 0.036 0.223 1676 Planarity : 0.003 0.042 1750 Dihedral : 7.797 57.536 2038 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.79 % Allowed : 13.11 % Favored : 85.09 % 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 aren not related in a simple way. whole: 2.12 (0.24), residues: 1254 helix: 2.26 (0.18), residues: 808 sheet: 1.37 (0.85), residues: 34 loop : -0.33 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.020 0.001 TYR A 331 PHE 0.009 0.001 PHE B 611 TRP 0.019 0.001 TRP B 342 HIS 0.002 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00244 (10872) covalent geometry : angle 0.47904 (14668) hydrogen bonds : bond 0.03408 ( 618) hydrogen bonds : angle 3.54031 ( 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 156 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.7059 (m-40) cc_final: 0.6370 (t0) REVERT: A 334 MET cc_start: 0.8320 (mmm) cc_final: 0.8119 (mmt) REVERT: A 339 MET cc_start: 0.8271 (ttm) cc_final: 0.7940 (ttm) REVERT: B 107 ASN cc_start: 0.7117 (m-40) cc_final: 0.6438 (t0) REVERT: B 339 MET cc_start: 0.8262 (ttm) cc_final: 0.7949 (ttm) REVERT: B 480 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8273 (pm20) outliers start: 19 outliers final: 14 residues processed: 148 average time/residue: 0.0937 time to fit residues: 20.6043 Evaluate side-chains 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 459 HIS B 67 GLN 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 = 0.3353 r_free = 0.3353 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.093021 restraints weight = 12750.117| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.83 r_work: 0.2745 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10872 Z= 0.172 Angle : 0.534 7.931 14668 Z= 0.264 Chirality : 0.038 0.231 1676 Planarity : 0.004 0.041 1750 Dihedral : 8.128 57.931 2038 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.42 % Allowed : 13.49 % Favored : 85.09 % 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 aren not related in a simple way. whole: 1.95 (0.24), residues: 1254 helix: 2.12 (0.18), residues: 804 sheet: 1.29 (0.86), 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 0.009 0.001 TYR B 308 PHE 0.011 0.001 PHE B 611 TRP 0.018 0.001 TRP B 342 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00407 (10872) covalent geometry : angle 0.53428 (14668) hydrogen bonds : bond 0.03878 ( 618) hydrogen bonds : angle 3.63726 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.12 seconds wall clock time: 42 minutes 46.67 seconds (2566.67 seconds total)