Starting phenix.real_space_refine on Wed Sep 17 20:16:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvx_38721/09_2025/8xvx_38721.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvx_38721/09_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_38721/09_2025/8xvx_38721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvx_38721/09_2025/8xvx_38721.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvx_38721/09_2025/8xvx_38721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvx_38721/09_2025/8xvx_38721.cif" } resolution = 3.32 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= 0.003 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): 0.01s 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: 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, 'ARG:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, '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, 'ARG:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 2.72, per 1000 atoms: 0.24 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: 1.13 Conformation dependent library (CDL) restraints added in 420.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.34 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: 1.81 Time building geometry restraints manager: 1.48 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 0.010 Normalize map: mean=0, sd=1: 0.950 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.310 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- 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 : 11.01 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 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: -0.50 (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 ARG 0.004 0.001 ARG B 682 TYR 0.055 0.002 TYR A 181 PHE 0.014 0.002 PHE A 593 TRP 0.017 0.002 TRP A 624 HIS 0.008 0.002 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00714 (11422) covalent geometry : angle 0.76435 (15550) hydrogen bonds : bond 0.13467 ( 735) hydrogen bonds : angle 5.75569 ( 2136) *********************** 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 : 0.348 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: 0.0750 time to fit residues: 22.9060 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 611 ASN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 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 = 0.3988 r_free = 0.3988 target = 0.174421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122101 restraints weight = 13219.321| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.63 r_work: 0.3205 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11422 Z= 0.158 Angle : 0.647 7.749 15550 Z= 0.340 Chirality : 0.044 0.206 1762 Planarity : 0.007 0.068 1944 Dihedral : 5.231 38.757 1494 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.29 % Allowed : 7.29 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.05 (0.23), residues: 1384 helix: 1.31 (0.17), residues: 956 sheet: -3.21 (0.82), residues: 30 loop : -3.26 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.038 0.002 TYR A 181 PHE 0.019 0.001 PHE B 428 TRP 0.015 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00357 (11422) covalent geometry : angle 0.64670 (15550) hydrogen bonds : bond 0.04824 ( 735) hydrogen bonds : angle 4.78233 ( 2136) *********************** 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 176 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 151 ASN cc_start: 0.7137 (t0) cc_final: 0.6621 (t0) REVERT: B 165 MET cc_start: 0.7989 (mmp) cc_final: 0.7446 (mmm) REVERT: B 260 ASP cc_start: 0.7985 (t0) cc_final: 0.7778 (t0) REVERT: B 428 PHE cc_start: 0.8213 (t80) cc_final: 0.7951 (t80) REVERT: A 19 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7307 (t80) REVERT: A 31 GLN cc_start: 0.8076 (mm110) cc_final: 0.7871 (mm-40) REVERT: A 72 PHE cc_start: 0.7982 (p90) cc_final: 0.7682 (p90) REVERT: A 151 ASN cc_start: 0.6917 (t0) cc_final: 0.6630 (t0) REVERT: A 257 ASN cc_start: 0.8547 (m110) cc_final: 0.8234 (m110) REVERT: A 260 ASP cc_start: 0.8146 (t0) cc_final: 0.7895 (t0) REVERT: A 589 MET cc_start: 0.8220 (ttt) cc_final: 0.8017 (ttp) outliers start: 15 outliers final: 13 residues processed: 171 average time/residue: 0.0728 time to fit residues: 20.0480 Evaluate side-chains 159 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 611 ASN A 639 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125398 restraints weight = 13394.692| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.46 r_work: 0.3230 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1386 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= 0.146 Angle : 0.604 8.987 15550 Z= 0.315 Chirality : 0.043 0.191 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.998 37.292 1494 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.80 % Allowed : 9.86 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.19 (0.24), residues: 1384 helix: 1.49 (0.17), residues: 956 sheet: -2.91 (0.85), residues: 30 loop : -3.17 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.031 0.001 TYR A 181 PHE 0.016 0.001 PHE B 21 TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00332 (11422) covalent geometry : angle 0.60382 (15550) hydrogen bonds : bond 0.04467 ( 735) hydrogen bonds : angle 4.63011 ( 2136) *********************** 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 : 0.376 Fit side-chains REVERT: B 151 ASN cc_start: 0.7087 (t0) cc_final: 0.6608 (t0) REVERT: B 157 MET cc_start: 0.4142 (tmm) cc_final: 0.3719 (tmm) REVERT: B 260 ASP cc_start: 0.8000 (t0) cc_final: 0.7708 (t0) REVERT: B 521 MET cc_start: 0.8184 (ttm) cc_final: 0.7833 (ttp) REVERT: B 587 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 19 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7332 (t80) REVERT: A 72 PHE cc_start: 0.8065 (p90) cc_final: 0.7759 (p90) REVERT: A 151 ASN cc_start: 0.6903 (t0) cc_final: 0.6627 (t0) REVERT: A 257 ASN cc_start: 0.8511 (m110) cc_final: 0.8234 (m110) REVERT: A 260 ASP cc_start: 0.8212 (t0) cc_final: 0.7912 (t0) REVERT: A 534 MET cc_start: 0.7920 (mmm) cc_final: 0.7687 (mtt) outliers start: 21 outliers final: 16 residues processed: 171 average time/residue: 0.0793 time to fit residues: 21.9078 Evaluate side-chains 165 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 1 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.6382 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.172954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123382 restraints weight = 13458.837| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.23 r_work: 0.3189 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11422 Z= 0.196 Angle : 0.638 9.437 15550 Z= 0.331 Chirality : 0.044 0.196 1762 Planarity : 0.006 0.069 1944 Dihedral : 4.981 38.134 1494 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.23 % Allowed : 14.32 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.20 (0.24), residues: 1384 helix: 1.50 (0.17), residues: 956 sheet: -3.00 (0.83), residues: 30 loop : -3.17 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.034 0.002 TYR A 181 PHE 0.018 0.001 PHE B 21 TRP 0.019 0.001 TRP B 624 HIS 0.006 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00471 (11422) covalent geometry : angle 0.63797 (15550) hydrogen bonds : bond 0.04647 ( 735) hydrogen bonds : angle 4.67646 ( 2136) *********************** 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 180 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.478 Fit side-chains REVERT: B 151 ASN cc_start: 0.7095 (t0) cc_final: 0.6621 (t0) REVERT: B 157 MET cc_start: 0.3950 (tmm) cc_final: 0.3499 (tmm) REVERT: B 263 GLN cc_start: 0.8135 (mt0) cc_final: 0.7683 (mt0) REVERT: B 521 MET cc_start: 0.8316 (ttm) cc_final: 0.7945 (ttp) REVERT: B 587 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 19 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7291 (t80) REVERT: A 72 PHE cc_start: 0.8019 (p90) cc_final: 0.7747 (p90) REVERT: A 151 ASN cc_start: 0.6970 (t0) cc_final: 0.6704 (t0) REVERT: A 257 ASN cc_start: 0.8481 (m110) cc_final: 0.8226 (m110) REVERT: A 260 ASP cc_start: 0.8159 (t0) cc_final: 0.7861 (t0) REVERT: A 378 MET cc_start: 0.7178 (mmm) cc_final: 0.6510 (mmm) REVERT: A 534 MET cc_start: 0.7891 (mmm) cc_final: 0.7684 (mtt) REVERT: A 589 MET cc_start: 0.8163 (ttt) cc_final: 0.7951 (ttp) outliers start: 26 outliers final: 19 residues processed: 170 average time/residue: 0.0744 time to fit residues: 20.6603 Evaluate side-chains 168 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 444 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.0010 chunk 122 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.176203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124389 restraints weight = 13226.719| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.82 r_work: 0.3218 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1688 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= 0.144 Angle : 0.597 9.850 15550 Z= 0.308 Chirality : 0.042 0.191 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.853 36.424 1494 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.23 % Allowed : 15.87 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.36 (0.24), residues: 1384 helix: 1.62 (0.17), residues: 956 sheet: -2.97 (0.86), residues: 30 loop : -3.10 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 TYR 0.028 0.001 TYR B 181 PHE 0.018 0.001 PHE B 21 TRP 0.016 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00331 (11422) covalent geometry : angle 0.59653 (15550) hydrogen bonds : bond 0.04277 ( 735) hydrogen bonds : angle 4.55241 ( 2136) *********************** 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: 26 poor density : 156 time to evaluate : 0.473 Fit side-chains REVERT: B 151 ASN cc_start: 0.7042 (t0) cc_final: 0.6577 (t0) REVERT: B 157 MET cc_start: 0.3855 (tmm) cc_final: 0.3503 (tmm) REVERT: B 521 MET cc_start: 0.8322 (ttm) cc_final: 0.7948 (ttp) REVERT: B 587 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8638 (p) REVERT: A 19 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7312 (t80) REVERT: A 72 PHE cc_start: 0.7997 (p90) cc_final: 0.7718 (p90) REVERT: A 151 ASN cc_start: 0.7060 (t0) cc_final: 0.6771 (t0) REVERT: A 257 ASN cc_start: 0.8457 (m110) cc_final: 0.8202 (m110) REVERT: A 260 ASP cc_start: 0.8143 (t0) cc_final: 0.7881 (t0) REVERT: A 534 MET cc_start: 0.7835 (mmm) cc_final: 0.7629 (mtt) outliers start: 26 outliers final: 20 residues processed: 171 average time/residue: 0.0754 time to fit residues: 21.1341 Evaluate side-chains 171 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 429 LEU Chi-restraints excluded: chain B residue 514 THR 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 520 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 49 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 0.0870 chunk 115 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.177831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128229 restraints weight = 13328.744| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.32 r_work: 0.3278 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1882 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= 0.129 Angle : 0.587 9.683 15550 Z= 0.301 Chirality : 0.042 0.191 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.723 34.836 1494 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.23 % Allowed : 16.64 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.48 (0.24), residues: 1384 helix: 1.69 (0.17), residues: 960 sheet: -2.88 (0.89), residues: 30 loop : -3.06 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.020 0.001 TYR B 181 PHE 0.018 0.001 PHE B 21 TRP 0.016 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00289 (11422) covalent geometry : angle 0.58742 (15550) hydrogen bonds : bond 0.04053 ( 735) hydrogen bonds : angle 4.45746 ( 2136) *********************** 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 189 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.377 Fit side-chains REVERT: B 151 ASN cc_start: 0.6985 (t0) cc_final: 0.6502 (t0) REVERT: B 157 MET cc_start: 0.3677 (tmm) cc_final: 0.3374 (tmm) REVERT: B 521 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7958 (ttp) REVERT: A 23 ILE cc_start: 0.9112 (mm) cc_final: 0.8890 (mm) REVERT: A 117 TRP cc_start: 0.7989 (m100) cc_final: 0.7591 (m100) REVERT: A 151 ASN cc_start: 0.6950 (t0) cc_final: 0.6670 (t0) REVERT: A 257 ASN cc_start: 0.8431 (m110) cc_final: 0.8201 (m110) REVERT: A 260 ASP cc_start: 0.8189 (t0) cc_final: 0.7933 (t0) REVERT: A 521 MET cc_start: 0.8170 (ttp) cc_final: 0.7811 (ttp) REVERT: A 587 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8466 (p) outliers start: 26 outliers final: 20 residues processed: 179 average time/residue: 0.0795 time to fit residues: 23.3003 Evaluate side-chains 173 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 521 MET 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 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 57 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.177382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126505 restraints weight = 13319.473| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.53 r_work: 0.3246 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1951 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= 0.140 Angle : 0.593 9.649 15550 Z= 0.303 Chirality : 0.042 0.190 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.693 34.649 1494 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.74 % Allowed : 18.18 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.47 (0.24), residues: 1384 helix: 1.71 (0.17), residues: 950 sheet: -2.73 (0.91), residues: 30 loop : -3.04 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.022 0.001 TYR A 181 PHE 0.014 0.001 PHE B 21 TRP 0.017 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00324 (11422) covalent geometry : angle 0.59343 (15550) hydrogen bonds : bond 0.04101 ( 735) hydrogen bonds : angle 4.45236 ( 2136) *********************** 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 185 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.489 Fit side-chains REVERT: B 78 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 151 ASN cc_start: 0.7053 (t0) cc_final: 0.6604 (t0) REVERT: B 157 MET cc_start: 0.3842 (tmm) cc_final: 0.3527 (tmm) REVERT: B 167 TYR cc_start: 0.8299 (m-80) cc_final: 0.7974 (m-80) REVERT: B 222 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: B 521 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7907 (ttp) REVERT: B 587 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8716 (p) REVERT: A 78 GLU cc_start: 0.7824 (pp20) cc_final: 0.7437 (pp20) REVERT: A 117 TRP cc_start: 0.7929 (m100) cc_final: 0.7507 (m100) REVERT: A 151 ASN cc_start: 0.7080 (t0) cc_final: 0.6817 (t0) REVERT: A 155 TYR cc_start: 0.5808 (t80) cc_final: 0.5310 (t80) REVERT: A 257 ASN cc_start: 0.8367 (m110) cc_final: 0.8133 (m110) REVERT: A 260 ASP cc_start: 0.8138 (t0) cc_final: 0.7880 (t0) REVERT: A 378 MET cc_start: 0.6887 (mmm) cc_final: 0.6505 (mmm) REVERT: A 521 MET cc_start: 0.8141 (ttp) cc_final: 0.7785 (ttp) REVERT: A 587 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 589 MET cc_start: 0.7916 (ttt) cc_final: 0.7608 (ttp) outliers start: 32 outliers final: 24 residues processed: 175 average time/residue: 0.0743 time to fit residues: 21.3995 Evaluate side-chains 178 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 37 VAL 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 521 MET 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 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 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 137 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.177409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130069 restraints weight = 13208.446| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.23 r_work: 0.3264 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2020 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= 0.140 Angle : 0.601 10.306 15550 Z= 0.305 Chirality : 0.042 0.192 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.656 34.455 1494 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.66 % Allowed : 18.35 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.52 (0.24), residues: 1384 helix: 1.70 (0.17), residues: 960 sheet: -2.72 (0.90), residues: 30 loop : -3.01 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.022 0.001 TYR A 181 PHE 0.013 0.001 PHE B 21 TRP 0.016 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00325 (11422) covalent geometry : angle 0.60117 (15550) hydrogen bonds : bond 0.04086 ( 735) hydrogen bonds : angle 4.44036 ( 2136) *********************** 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 185 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.454 Fit side-chains REVERT: B 78 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 151 ASN cc_start: 0.7077 (t0) cc_final: 0.6625 (t0) REVERT: B 157 MET cc_start: 0.3920 (tmm) cc_final: 0.3594 (tmm) REVERT: B 167 TYR cc_start: 0.8337 (m-80) cc_final: 0.8029 (m-80) REVERT: B 222 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: B 378 MET cc_start: 0.7224 (mmm) cc_final: 0.6984 (mmm) REVERT: B 521 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7944 (ttp) REVERT: B 587 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8752 (p) REVERT: A 19 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7238 (t80) REVERT: A 78 GLU cc_start: 0.7717 (pp20) cc_final: 0.7362 (pp20) REVERT: A 151 ASN cc_start: 0.7117 (t0) cc_final: 0.6868 (t0) REVERT: A 155 TYR cc_start: 0.5966 (t80) cc_final: 0.5176 (t80) REVERT: A 165 MET cc_start: 0.7998 (mmp) cc_final: 0.7552 (mmm) REVERT: A 257 ASN cc_start: 0.8330 (m110) cc_final: 0.8109 (m110) REVERT: A 260 ASP cc_start: 0.8176 (t0) cc_final: 0.7918 (t0) REVERT: A 378 MET cc_start: 0.7198 (mmm) cc_final: 0.6669 (mmm) REVERT: A 521 MET cc_start: 0.8178 (ttp) cc_final: 0.7853 (ttp) REVERT: A 547 PHE cc_start: 0.7828 (m-10) cc_final: 0.7596 (m-10) REVERT: A 587 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 589 MET cc_start: 0.8044 (ttt) cc_final: 0.7753 (ttp) outliers start: 31 outliers final: 22 residues processed: 176 average time/residue: 0.0739 time to fit residues: 21.4864 Evaluate side-chains 178 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 37 VAL 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 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 521 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.177780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128373 restraints weight = 13101.101| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.23 r_work: 0.3261 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2100 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= 0.138 Angle : 0.603 10.026 15550 Z= 0.306 Chirality : 0.042 0.191 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.625 34.125 1494 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.32 % Allowed : 18.61 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.50 (0.24), residues: 1384 helix: 1.73 (0.17), residues: 948 sheet: -2.73 (0.91), residues: 30 loop : -3.01 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.020 0.001 TYR A 181 PHE 0.012 0.001 PHE A 72 TRP 0.015 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00319 (11422) covalent geometry : angle 0.60318 (15550) hydrogen bonds : bond 0.04062 ( 735) hydrogen bonds : angle 4.42527 ( 2136) *********************** 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 181 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.414 Fit side-chains REVERT: B 78 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 151 ASN cc_start: 0.7087 (t0) cc_final: 0.6665 (t0) REVERT: B 157 MET cc_start: 0.3809 (tmm) cc_final: 0.3492 (tmm) REVERT: B 222 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: B 378 MET cc_start: 0.7176 (mmm) cc_final: 0.6924 (mmm) REVERT: B 521 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7908 (ttp) REVERT: B 587 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8738 (p) REVERT: A 19 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7217 (t80) REVERT: A 78 GLU cc_start: 0.7731 (pp20) cc_final: 0.7366 (pp20) REVERT: A 151 ASN cc_start: 0.7097 (t0) cc_final: 0.6853 (t0) REVERT: A 165 MET cc_start: 0.7975 (mmp) cc_final: 0.7535 (mmm) REVERT: A 257 ASN cc_start: 0.8314 (m110) cc_final: 0.8095 (m110) REVERT: A 260 ASP cc_start: 0.8207 (t0) cc_final: 0.7953 (t0) REVERT: A 378 MET cc_start: 0.7011 (mmm) cc_final: 0.6741 (mmm) REVERT: A 521 MET cc_start: 0.8150 (ttp) cc_final: 0.7817 (ttp) REVERT: A 587 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8474 (p) REVERT: A 589 MET cc_start: 0.8033 (ttt) cc_final: 0.7729 (ttp) outliers start: 27 outliers final: 20 residues processed: 171 average time/residue: 0.0767 time to fit residues: 21.5200 Evaluate side-chains 177 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 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 521 MET 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 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 533 LEU Chi-restraints excluded: chain A residue 587 THR 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 29 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 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** A 639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130993 restraints weight = 13281.297| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.19 r_work: 0.3286 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2216 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= 0.130 Angle : 0.603 11.277 15550 Z= 0.302 Chirality : 0.042 0.191 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.563 33.402 1494 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.14 % Allowed : 18.78 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.60 (0.24), residues: 1384 helix: 1.88 (0.17), residues: 932 sheet: -2.66 (0.91), residues: 30 loop : -2.97 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.018 0.001 TYR B 181 PHE 0.012 0.001 PHE A 493 TRP 0.014 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00294 (11422) covalent geometry : angle 0.60318 (15550) hydrogen bonds : bond 0.03965 ( 735) hydrogen bonds : angle 4.38959 ( 2136) ********************** 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 183 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.519 Fit side-chains REVERT: B 78 GLU cc_start: 0.8240 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 151 ASN cc_start: 0.6999 (t0) cc_final: 0.6585 (t0) REVERT: B 157 MET cc_start: 0.3595 (tmm) cc_final: 0.3376 (tmm) REVERT: B 222 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: B 378 MET cc_start: 0.7214 (mmm) cc_final: 0.7011 (mmm) REVERT: B 449 SER cc_start: 0.8944 (m) cc_final: 0.8574 (p) REVERT: B 521 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7911 (ttp) REVERT: B 587 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 19 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7302 (t80) REVERT: A 78 GLU cc_start: 0.7915 (pp20) cc_final: 0.7494 (pp20) REVERT: A 151 ASN cc_start: 0.6961 (t0) cc_final: 0.6714 (t0) REVERT: A 165 MET cc_start: 0.8080 (mmp) cc_final: 0.7637 (mmm) REVERT: A 257 ASN cc_start: 0.8370 (m110) cc_final: 0.8130 (m110) REVERT: A 260 ASP cc_start: 0.8251 (t0) cc_final: 0.8005 (t0) REVERT: A 378 MET cc_start: 0.7108 (mmm) cc_final: 0.6844 (mmm) REVERT: A 521 MET cc_start: 0.8216 (ttp) cc_final: 0.7876 (ttp) REVERT: A 587 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8399 (p) outliers start: 25 outliers final: 20 residues processed: 175 average time/residue: 0.0771 time to fit residues: 22.1685 Evaluate side-chains 183 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 521 MET 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 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 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 107 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.174323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119364 restraints weight = 13373.693| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.23 r_work: 0.3210 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11422 Z= 0.183 Angle : 0.632 9.986 15550 Z= 0.323 Chirality : 0.044 0.194 1762 Planarity : 0.006 0.068 1944 Dihedral : 4.654 35.533 1494 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.40 % Allowed : 18.44 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.41 (0.24), residues: 1384 helix: 1.71 (0.17), residues: 948 sheet: -2.76 (0.92), residues: 30 loop : -3.18 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.030 0.002 TYR A 181 PHE 0.012 0.001 PHE A 493 TRP 0.018 0.001 TRP B 624 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00440 (11422) covalent geometry : angle 0.63239 (15550) hydrogen bonds : bond 0.04384 ( 735) hydrogen bonds : angle 4.51155 ( 2136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.76 seconds wall clock time: 44 minutes 35.55 seconds (2675.55 seconds total)