Starting phenix.real_space_refine on Tue Jul 29 06:03:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvx_38721/07_2025/8xvx_38721.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvx_38721/07_2025/8xvx_38721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvx_38721/07_2025/8xvx_38721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvx_38721/07_2025/8xvx_38721.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvx_38721/07_2025/8xvx_38721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvx_38721/07_2025/8xvx_38721.cif" } resolution = 3.32 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= 0.003 sd= 0.085 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7350 2.51 5 N 1810 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11110 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5555 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 36, 'TRANS': 659} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5555 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 36, 'TRANS': 659} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 6.59, per 1000 atoms: 0.59 Number of scatterers: 11110 At special positions: 0 Unit cell: (88.62, 143.48, 108.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1900 8.00 N 1810 7.00 C 7350 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: 2.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 2 sheets defined 76.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 3 through 31 removed outlier: 3.573A pdb=" N GLN B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.624A pdb=" N GLU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.928A pdb=" N ASP B 89 " --> pdb=" O PRO B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.552A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Proline residue: B 111 - end of helix Proline residue: B 122 - end of helix removed outlier: 3.521A pdb=" N THR B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 136 removed outlier: 4.276A pdb=" N MET B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 155 through 193 removed outlier: 3.755A pdb=" N PHE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.949A pdb=" N LEU B 283 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 284 " --> pdb=" O LEU B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 284' Processing helix chain 'B' and resid 290 through 314 removed outlier: 3.779A pdb=" N TYR B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 360 through 366 removed outlier: 4.145A pdb=" N ALA B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 366 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 398 Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 399 through 408 removed outlier: 4.306A pdb=" N GLY B 404 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 406 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 4.513A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 440 Proline residue: B 430 - end of helix removed outlier: 4.493A pdb=" N PHE B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.602A pdb=" N ILE B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 452 " --> pdb=" O MET B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 489 Processing helix chain 'B' and resid 489 through 495 removed outlier: 4.679A pdb=" N ASN B 495 " --> pdb=" O ASN B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 534 removed outlier: 4.217A pdb=" N ILE B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Proline residue: B 510 - end of helix removed outlier: 3.785A pdb=" N THR B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 547 removed outlier: 3.579A pdb=" N LEU B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 565 through 587 Proline residue: B 571 - end of helix Proline residue: B 585 - end of helix Processing helix chain 'B' and resid 590 through 611 removed outlier: 3.841A pdb=" N ILE B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 Processing helix chain 'B' and resid 653 through 658 removed outlier: 3.614A pdb=" N PHE B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 removed outlier: 4.111A pdb=" N ILE B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.789A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 Processing helix chain 'A' and resid 4 through 31 removed outlier: 3.574A pdb=" N GLN A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.624A pdb=" N GLU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 3.927A pdb=" N ASP A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 126 removed outlier: 3.551A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Proline residue: A 111 - end of helix Proline residue: A 122 - end of helix removed outlier: 3.520A pdb=" N THR A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 removed outlier: 4.276A pdb=" N MET A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 155 through 193 removed outlier: 3.756A pdb=" N PHE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.949A pdb=" N LEU A 283 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 284 " --> pdb=" O LEU A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.779A pdb=" N TYR A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 360 through 366 removed outlier: 4.144A pdb=" N ALA A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 399 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 408 removed outlier: 4.305A pdb=" N GLY A 404 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 4.514A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 440 Proline residue: A 430 - end of helix removed outlier: 4.493A pdb=" N PHE A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.602A pdb=" N ILE A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 489 Processing helix chain 'A' and resid 489 through 495 removed outlier: 4.678A pdb=" N ASN A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 534 removed outlier: 4.217A pdb=" N ILE A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Proline residue: A 510 - end of helix removed outlier: 3.785A pdb=" N THR A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 547 removed outlier: 3.580A pdb=" N LEU A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 565 through 587 Proline residue: A 571 - end of helix Proline residue: A 585 - end of helix Processing helix chain 'A' and resid 590 through 611 removed outlier: 3.841A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.613A pdb=" N PHE A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 4.112A pdb=" N ILE A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.789A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 Processing sheet with id=AA1, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.545A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 351 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.543A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 351 " --> pdb=" O LEU A 205 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2136 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: 3.51 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3409 1.34 - 1.46: 1875 1.46 - 1.57: 6046 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11422 Sorted by residual: bond pdb=" CA THR A 401 " pdb=" C THR A 401 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.62e+00 bond pdb=" CA THR B 401 " pdb=" C THR B 401 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.34e-02 5.57e+03 2.49e+00 bond pdb=" CB CYS A 672 " pdb=" SG CYS A 672 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB CYS B 672 " pdb=" SG CYS B 672 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CE1 TYR B 181 " pdb=" CZ TYR B 181 " ideal model delta sigma weight residual 1.378 1.344 0.034 2.40e-02 1.74e+03 2.04e+00 ... (remaining 11417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 14389 1.26 - 2.53: 877 2.53 - 3.79: 204 3.79 - 5.05: 62 5.05 - 6.31: 18 Bond angle restraints: 15550 Sorted by residual: angle pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" C ASN B 128 " ideal model delta sigma weight residual 114.62 110.19 4.43 1.14e+00 7.69e-01 1.51e+01 angle pdb=" N ASN A 128 " pdb=" CA ASN A 128 " pdb=" C ASN A 128 " ideal model delta sigma weight residual 114.62 110.22 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N PRO B 715 " pdb=" CA PRO B 715 " pdb=" C PRO B 715 " ideal model delta sigma weight residual 112.47 118.68 -6.21 2.06e+00 2.36e-01 9.08e+00 angle pdb=" N PRO A 715 " pdb=" CA PRO A 715 " pdb=" C PRO A 715 " ideal model delta sigma weight residual 112.47 118.59 -6.12 2.06e+00 2.36e-01 8.82e+00 angle pdb=" N LYS A 673 " pdb=" CA LYS A 673 " pdb=" C LYS A 673 " ideal model delta sigma weight residual 111.02 107.85 3.17 1.22e+00 6.72e-01 6.74e+00 ... (remaining 15545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 5861 15.85 - 31.70: 661 31.70 - 47.56: 168 47.56 - 63.41: 24 63.41 - 79.26: 16 Dihedral angle restraints: 6730 sinusoidal: 2612 harmonic: 4118 Sorted by residual: dihedral pdb=" CA LEU B 548 " pdb=" C LEU B 548 " pdb=" N VAL B 549 " pdb=" CA VAL B 549 " ideal model delta harmonic sigma weight residual 180.00 -143.06 -36.94 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA LEU A 548 " pdb=" C LEU A 548 " pdb=" N VAL A 549 " pdb=" CA VAL A 549 " ideal model delta harmonic sigma weight residual -180.00 -143.07 -36.93 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA ARG B 207 " pdb=" C ARG B 207 " pdb=" N ASN B 208 " pdb=" CA ASN B 208 " ideal model delta harmonic sigma weight residual 180.00 143.37 36.63 0 5.00e+00 4.00e-02 5.37e+01 ... (remaining 6727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1147 0.043 - 0.087: 462 0.087 - 0.130: 123 0.130 - 0.173: 20 0.173 - 0.216: 10 Chirality restraints: 1762 Sorted by residual: chirality pdb=" CB THR B 587 " pdb=" CA THR B 587 " pdb=" OG1 THR B 587 " pdb=" CG2 THR B 587 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR A 587 " pdb=" CA THR A 587 " pdb=" OG1 THR A 587 " pdb=" CG2 THR A 587 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA THR B 110 " pdb=" N THR B 110 " pdb=" C THR B 110 " pdb=" CB THR B 110 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1759 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 181 " 0.028 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR A 181 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 181 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 181 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 181 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 181 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 181 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " 0.028 2.00e-02 2.50e+03 2.25e-02 1.02e+01 pdb=" CG TYR B 181 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 624 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 625 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " 0.037 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 268 2.69 - 3.24: 11718 3.24 - 3.79: 17891 3.79 - 4.35: 22295 4.35 - 4.90: 38118 Nonbonded interactions: 90290 Sorted by model distance: nonbonded pdb=" O MET B 82 " pdb=" NH2 ARG B 606 " model vdw 2.136 3.120 nonbonded pdb=" O MET A 82 " pdb=" NH2 ARG A 606 " model vdw 2.137 3.120 nonbonded pdb=" OH TYR A 167 " pdb=" O PHE A 657 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 167 " pdb=" O PHE B 657 " model vdw 2.219 3.040 nonbonded pdb=" O PHE A 420 " pdb=" OG SER A 423 " model vdw 2.237 3.040 ... (remaining 90285 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' selection = chain 'B' } 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: 0.840 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.007 0.059 11422 Z= 0.301 Angle : 0.764 6.313 15550 Z= 0.430 Chirality : 0.050 0.216 1762 Planarity : 0.007 0.065 1944 Dihedral : 14.523 79.260 4054 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.50 (0.23), residues: 1384 helix: 0.98 (0.17), residues: 940 sheet: -3.31 (0.85), residues: 30 loop : -3.27 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 624 HIS 0.008 0.002 HIS B 229 PHE 0.014 0.002 PHE A 593 TYR 0.055 0.002 TYR A 181 ARG 0.004 0.001 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.13467 ( 735) hydrogen bonds : angle 5.75569 ( 2136) covalent geometry : bond 0.00714 (11422) covalent geometry : angle 0.76435 (15550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.236 Fit side-chains REVERT: B 376 LEU cc_start: 0.8419 (mt) cc_final: 0.8217 (mp) REVERT: B 659 ILE cc_start: 0.8501 (tp) cc_final: 0.8246 (tp) REVERT: A 151 ASN cc_start: 0.6780 (t0) cc_final: 0.6519 (t0) REVERT: A 257 ASN cc_start: 0.8542 (m110) cc_final: 0.8328 (m110) REVERT: A 378 MET cc_start: 0.6996 (mmm) cc_final: 0.6181 (mmm) REVERT: A 643 MET cc_start: 0.7433 (ttp) cc_final: 0.7065 (ttt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1655 time to fit residues: 49.3311 Evaluate side-chains 153 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 0.0050 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 0.0170 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN B 611 ASN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124380 restraints weight = 13140.357| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.41 r_work: 0.3254 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11422 Z= 0.144 Angle : 0.635 8.015 15550 Z= 0.334 Chirality : 0.044 0.207 1762 Planarity : 0.007 0.068 1944 Dihedral : 5.205 38.069 1494 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.54 % Allowed : 7.29 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.09 (0.24), residues: 1384 helix: 1.43 (0.17), residues: 944 sheet: -3.17 (0.83), residues: 30 loop : -3.11 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 624 HIS 0.003 0.001 HIS A 628 PHE 0.017 0.001 PHE B 428 TYR 0.034 0.002 TYR A 181 ARG 0.002 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 735) hydrogen bonds : angle 4.73751 ( 2136) covalent geometry : bond 0.00313 (11422) covalent geometry : angle 0.63518 (15550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: B 151 ASN cc_start: 0.7104 (t0) cc_final: 0.6578 (t0) REVERT: B 165 MET cc_start: 0.8135 (mmp) cc_final: 0.7694 (mmm) REVERT: B 260 ASP cc_start: 0.8090 (t0) cc_final: 0.7881 (t0) REVERT: B 449 SER cc_start: 0.8941 (m) cc_final: 0.8538 (p) REVERT: A 19 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7384 (t80) REVERT: A 31 GLN cc_start: 0.8121 (mm110) cc_final: 0.7915 (mm-40) REVERT: A 72 PHE cc_start: 0.8110 (p90) cc_final: 0.7796 (p90) REVERT: A 151 ASN cc_start: 0.6883 (t0) cc_final: 0.6585 (t0) REVERT: A 257 ASN cc_start: 0.8553 (m110) cc_final: 0.8257 (m110) REVERT: A 260 ASP cc_start: 0.8243 (t0) cc_final: 0.8000 (t0) outliers start: 18 outliers final: 14 residues processed: 177 average time/residue: 0.1680 time to fit residues: 47.5516 Evaluate side-chains 163 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 118 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.125647 restraints weight = 13332.537| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.39 r_work: 0.3217 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11422 Z= 0.157 Angle : 0.608 8.628 15550 Z= 0.318 Chirality : 0.043 0.191 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.993 37.402 1494 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 1.80 % Allowed : 9.95 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.19 (0.24), residues: 1384 helix: 1.49 (0.17), residues: 958 sheet: -2.89 (0.84), residues: 30 loop : -3.20 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.005 0.001 HIS B 229 PHE 0.016 0.001 PHE B 21 TYR 0.033 0.001 TYR A 181 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 735) hydrogen bonds : angle 4.64080 ( 2136) covalent geometry : bond 0.00365 (11422) covalent geometry : angle 0.60790 (15550) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: B 151 ASN cc_start: 0.7076 (t0) cc_final: 0.6600 (t0) REVERT: B 157 MET cc_start: 0.4015 (tmm) cc_final: 0.3639 (tmm) REVERT: B 260 ASP cc_start: 0.7979 (t0) cc_final: 0.7692 (t0) REVERT: B 587 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8657 (p) REVERT: A 19 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7298 (t80) REVERT: A 72 PHE cc_start: 0.8080 (p90) cc_final: 0.7764 (p90) REVERT: A 151 ASN cc_start: 0.6862 (t0) cc_final: 0.6580 (t0) REVERT: A 257 ASN cc_start: 0.8521 (m110) cc_final: 0.8227 (m110) REVERT: A 260 ASP cc_start: 0.8190 (t0) cc_final: 0.7893 (t0) REVERT: A 378 MET cc_start: 0.7052 (mmm) cc_final: 0.6434 (mmm) outliers start: 21 outliers final: 16 residues processed: 171 average time/residue: 0.1768 time to fit residues: 48.6532 Evaluate side-chains 163 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.173508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124334 restraints weight = 13322.990| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.14 r_work: 0.3197 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11422 Z= 0.186 Angle : 0.627 9.301 15550 Z= 0.325 Chirality : 0.044 0.195 1762 Planarity : 0.006 0.069 1944 Dihedral : 4.956 38.046 1494 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.23 % Allowed : 14.41 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.23 (0.24), residues: 1384 helix: 1.51 (0.17), residues: 956 sheet: -3.02 (0.82), residues: 30 loop : -3.13 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 624 HIS 0.006 0.001 HIS A 628 PHE 0.016 0.001 PHE B 21 TYR 0.036 0.002 TYR A 181 ARG 0.003 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 735) hydrogen bonds : angle 4.65982 ( 2136) covalent geometry : bond 0.00445 (11422) covalent geometry : angle 0.62694 (15550) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 151 ASN cc_start: 0.7142 (t0) cc_final: 0.6675 (t0) REVERT: B 157 MET cc_start: 0.3771 (tmm) cc_final: 0.3355 (tmm) REVERT: B 260 ASP cc_start: 0.8145 (t0) cc_final: 0.7839 (t0) REVERT: B 521 MET cc_start: 0.8231 (ttm) cc_final: 0.8002 (ttp) REVERT: B 587 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8648 (p) REVERT: A 19 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 72 PHE cc_start: 0.8055 (p90) cc_final: 0.7772 (p90) REVERT: A 151 ASN cc_start: 0.6862 (t0) cc_final: 0.6584 (t0) REVERT: A 165 MET cc_start: 0.8035 (mmp) cc_final: 0.7711 (mmm) REVERT: A 257 ASN cc_start: 0.8481 (m110) cc_final: 0.8229 (m110) REVERT: A 260 ASP cc_start: 0.8222 (t0) cc_final: 0.7968 (t0) REVERT: A 521 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7908 (ttp) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.1606 time to fit residues: 44.2137 Evaluate side-chains 170 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.176546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126791 restraints weight = 13158.115| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.34 r_work: 0.3235 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11422 Z= 0.143 Angle : 0.592 9.611 15550 Z= 0.306 Chirality : 0.042 0.191 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.814 36.317 1494 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.14 % Allowed : 16.30 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.37 (0.24), residues: 1384 helix: 1.61 (0.17), residues: 958 sheet: -3.01 (0.85), residues: 30 loop : -3.10 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.017 0.001 PHE B 21 TYR 0.028 0.001 TYR B 181 ARG 0.003 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 735) hydrogen bonds : angle 4.53774 ( 2136) covalent geometry : bond 0.00328 (11422) covalent geometry : angle 0.59192 (15550) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.269 Fit side-chains REVERT: B 151 ASN cc_start: 0.7057 (t0) cc_final: 0.6575 (t0) REVERT: B 157 MET cc_start: 0.3908 (tmm) cc_final: 0.3548 (tmm) REVERT: B 260 ASP cc_start: 0.7974 (t0) cc_final: 0.7655 (t0) REVERT: B 521 MET cc_start: 0.7966 (ttm) cc_final: 0.7756 (ttp) REVERT: A 19 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7320 (t80) REVERT: A 72 PHE cc_start: 0.7924 (p90) cc_final: 0.7648 (p90) REVERT: A 151 ASN cc_start: 0.7070 (t0) cc_final: 0.6786 (t0) REVERT: A 257 ASN cc_start: 0.8414 (m110) cc_final: 0.8180 (m110) REVERT: A 260 ASP cc_start: 0.8135 (t0) cc_final: 0.7870 (t0) outliers start: 25 outliers final: 19 residues processed: 171 average time/residue: 0.1672 time to fit residues: 45.9749 Evaluate side-chains 168 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.177123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128831 restraints weight = 13271.654| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.32 r_work: 0.3235 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11422 Z= 0.136 Angle : 0.589 9.480 15550 Z= 0.302 Chirality : 0.042 0.191 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.723 35.482 1494 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.32 % Allowed : 16.90 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.42 (0.24), residues: 1384 helix: 1.65 (0.17), residues: 960 sheet: -2.92 (0.88), residues: 30 loop : -3.09 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.016 0.001 PHE B 21 TYR 0.023 0.001 TYR B 181 ARG 0.003 0.000 ARG B 555 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 735) hydrogen bonds : angle 4.47415 ( 2136) covalent geometry : bond 0.00313 (11422) covalent geometry : angle 0.58858 (15550) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 151 ASN cc_start: 0.7058 (t0) cc_final: 0.6585 (t0) REVERT: B 157 MET cc_start: 0.3856 (tmm) cc_final: 0.3531 (tmm) REVERT: B 260 ASP cc_start: 0.7959 (t0) cc_final: 0.7619 (t0) REVERT: B 521 MET cc_start: 0.7968 (ttm) cc_final: 0.7710 (ttp) REVERT: A 23 ILE cc_start: 0.9140 (mm) cc_final: 0.8914 (mm) REVERT: A 151 ASN cc_start: 0.7098 (t0) cc_final: 0.6824 (t0) REVERT: A 155 TYR cc_start: 0.5863 (t80) cc_final: 0.5133 (t80) REVERT: A 257 ASN cc_start: 0.8415 (m110) cc_final: 0.8181 (m110) REVERT: A 260 ASP cc_start: 0.8132 (t0) cc_final: 0.7875 (t0) REVERT: A 378 MET cc_start: 0.7220 (mmm) cc_final: 0.6705 (mmm) REVERT: A 521 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7777 (ttp) outliers start: 27 outliers final: 22 residues processed: 171 average time/residue: 0.1628 time to fit residues: 44.9195 Evaluate side-chains 172 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126764 restraints weight = 13363.532| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.52 r_work: 0.3254 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11422 Z= 0.135 Angle : 0.582 8.772 15550 Z= 0.298 Chirality : 0.042 0.191 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.654 34.713 1494 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.83 % Allowed : 17.75 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.50 (0.24), residues: 1384 helix: 1.74 (0.17), residues: 950 sheet: -2.83 (0.91), residues: 30 loop : -3.03 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.017 0.001 PHE B 21 TYR 0.021 0.001 TYR A 181 ARG 0.002 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 735) hydrogen bonds : angle 4.43953 ( 2136) covalent geometry : bond 0.00309 (11422) covalent geometry : angle 0.58174 (15550) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 151 ASN cc_start: 0.7066 (t0) cc_final: 0.6618 (t0) REVERT: B 157 MET cc_start: 0.3817 (tmm) cc_final: 0.3484 (tmm) REVERT: B 222 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: B 260 ASP cc_start: 0.7940 (t0) cc_final: 0.7598 (t0) REVERT: B 521 MET cc_start: 0.7946 (ttm) cc_final: 0.7637 (ttp) REVERT: B 587 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 117 TRP cc_start: 0.7936 (m100) cc_final: 0.7546 (m100) REVERT: A 151 ASN cc_start: 0.7058 (t0) cc_final: 0.6801 (t0) REVERT: A 165 MET cc_start: 0.7918 (mmp) cc_final: 0.7550 (mmm) REVERT: A 222 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8093 (tp30) REVERT: A 257 ASN cc_start: 0.8375 (m110) cc_final: 0.8141 (m110) REVERT: A 260 ASP cc_start: 0.8127 (t0) cc_final: 0.7873 (t0) REVERT: A 378 MET cc_start: 0.7062 (mmm) cc_final: 0.6708 (mmm) REVERT: A 521 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7806 (ttp) REVERT: A 587 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8433 (p) outliers start: 33 outliers final: 23 residues processed: 180 average time/residue: 0.1719 time to fit residues: 49.8701 Evaluate side-chains 181 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128379 restraints weight = 13254.693| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.31 r_work: 0.3280 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11422 Z= 0.129 Angle : 0.584 10.356 15550 Z= 0.295 Chirality : 0.041 0.191 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.583 33.690 1494 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.49 % Allowed : 18.27 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.57 (0.24), residues: 1384 helix: 1.74 (0.17), residues: 960 sheet: -2.66 (0.92), residues: 30 loop : -2.99 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.014 0.001 PHE B 21 TYR 0.019 0.001 TYR B 181 ARG 0.002 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 735) hydrogen bonds : angle 4.39118 ( 2136) covalent geometry : bond 0.00293 (11422) covalent geometry : angle 0.58367 (15550) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: B 151 ASN cc_start: 0.7032 (t0) cc_final: 0.6610 (t0) REVERT: B 157 MET cc_start: 0.3629 (tmm) cc_final: 0.3295 (tmm) REVERT: B 167 TYR cc_start: 0.8371 (m-80) cc_final: 0.8036 (m-80) REVERT: B 222 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: B 260 ASP cc_start: 0.8069 (t0) cc_final: 0.7729 (t0) REVERT: B 521 MET cc_start: 0.8078 (ttm) cc_final: 0.7752 (ttp) REVERT: B 587 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 19 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7240 (t80) REVERT: A 78 GLU cc_start: 0.7888 (pp20) cc_final: 0.7467 (pp20) REVERT: A 117 TRP cc_start: 0.8017 (m100) cc_final: 0.7642 (m100) REVERT: A 151 ASN cc_start: 0.6977 (t0) cc_final: 0.6723 (t0) REVERT: A 165 MET cc_start: 0.8082 (mmp) cc_final: 0.7648 (mmm) REVERT: A 222 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: A 257 ASN cc_start: 0.8380 (m110) cc_final: 0.8143 (m110) REVERT: A 260 ASP cc_start: 0.8251 (t0) cc_final: 0.7998 (t0) REVERT: A 521 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7934 (ttp) REVERT: A 587 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8414 (p) outliers start: 29 outliers final: 21 residues processed: 176 average time/residue: 0.1683 time to fit residues: 47.7012 Evaluate side-chains 180 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 96 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127638 restraints weight = 13233.981| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.77 r_work: 0.3236 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11422 Z= 0.143 Angle : 0.589 9.778 15550 Z= 0.300 Chirality : 0.042 0.189 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.582 34.079 1494 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.49 % Allowed : 18.18 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.45 (0.24), residues: 1384 helix: 1.71 (0.17), residues: 950 sheet: -2.73 (0.92), residues: 30 loop : -3.08 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 624 HIS 0.005 0.001 HIS A 628 PHE 0.013 0.001 PHE B 21 TYR 0.022 0.001 TYR A 181 ARG 0.002 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 735) hydrogen bonds : angle 4.41883 ( 2136) covalent geometry : bond 0.00336 (11422) covalent geometry : angle 0.58901 (15550) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: B 151 ASN cc_start: 0.7170 (t0) cc_final: 0.6755 (t0) REVERT: B 157 MET cc_start: 0.3773 (tmm) cc_final: 0.3466 (tmm) REVERT: B 222 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: B 260 ASP cc_start: 0.8001 (t0) cc_final: 0.7665 (t0) REVERT: B 378 MET cc_start: 0.7026 (mmm) cc_final: 0.6805 (mmm) REVERT: B 521 MET cc_start: 0.7998 (ttm) cc_final: 0.7673 (ttp) REVERT: B 587 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8683 (p) REVERT: A 19 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7205 (t80) REVERT: A 78 GLU cc_start: 0.7869 (pp20) cc_final: 0.7449 (pp20) REVERT: A 151 ASN cc_start: 0.7046 (t0) cc_final: 0.6815 (t0) REVERT: A 165 MET cc_start: 0.7972 (mmp) cc_final: 0.7509 (mmm) REVERT: A 222 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: A 257 ASN cc_start: 0.8360 (m110) cc_final: 0.8105 (m110) REVERT: A 260 ASP cc_start: 0.8178 (t0) cc_final: 0.7931 (t0) REVERT: A 378 MET cc_start: 0.7079 (mmm) cc_final: 0.6512 (mmm) REVERT: A 521 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7825 (ttp) REVERT: A 587 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8401 (p) outliers start: 29 outliers final: 21 residues processed: 175 average time/residue: 0.1611 time to fit residues: 45.3940 Evaluate side-chains 182 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.0040 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.179283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132014 restraints weight = 13245.893| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.10 r_work: 0.3295 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11422 Z= 0.125 Angle : 0.581 9.616 15550 Z= 0.295 Chirality : 0.042 0.190 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.499 32.957 1494 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.49 % Allowed : 18.61 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.59 (0.24), residues: 1384 helix: 1.87 (0.18), residues: 932 sheet: -2.58 (0.92), residues: 30 loop : -2.96 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.012 0.001 PHE A 493 TYR 0.017 0.001 TYR B 181 ARG 0.001 0.000 ARG B 555 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 735) hydrogen bonds : angle 4.35996 ( 2136) covalent geometry : bond 0.00282 (11422) covalent geometry : angle 0.58141 (15550) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: B 151 ASN cc_start: 0.7023 (t0) cc_final: 0.6611 (t0) REVERT: B 157 MET cc_start: 0.3584 (tmm) cc_final: 0.3359 (tmm) REVERT: B 222 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: B 260 ASP cc_start: 0.7991 (t0) cc_final: 0.7709 (t0) REVERT: B 521 MET cc_start: 0.8070 (ttm) cc_final: 0.7720 (ttp) REVERT: B 587 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 19 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7280 (t80) REVERT: A 78 GLU cc_start: 0.7953 (pp20) cc_final: 0.7528 (pp20) REVERT: A 151 ASN cc_start: 0.6971 (t0) cc_final: 0.6725 (t0) REVERT: A 165 MET cc_start: 0.8117 (mmp) cc_final: 0.7774 (mmm) REVERT: A 222 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: A 257 ASN cc_start: 0.8370 (m110) cc_final: 0.8132 (m110) REVERT: A 260 ASP cc_start: 0.8246 (t0) cc_final: 0.8002 (t0) REVERT: A 378 MET cc_start: 0.7185 (mmm) cc_final: 0.6732 (mmm) REVERT: A 521 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7870 (ttp) REVERT: A 587 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8434 (p) outliers start: 29 outliers final: 20 residues processed: 179 average time/residue: 0.1708 time to fit residues: 48.3974 Evaluate side-chains 182 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 109 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 128 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.179303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131675 restraints weight = 13260.797| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.20 r_work: 0.3288 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11422 Z= 0.127 Angle : 0.586 9.657 15550 Z= 0.297 Chirality : 0.042 0.189 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.477 32.604 1494 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.49 % Allowed : 18.61 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.24), residues: 1384 helix: 1.88 (0.17), residues: 932 sheet: -2.41 (0.95), residues: 30 loop : -2.97 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.012 0.001 PHE A 493 TYR 0.017 0.001 TYR B 181 ARG 0.006 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 735) hydrogen bonds : angle 4.36232 ( 2136) covalent geometry : bond 0.00289 (11422) covalent geometry : angle 0.58572 (15550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5614.56 seconds wall clock time: 97 minutes 16.69 seconds (5836.69 seconds total)