Starting phenix.real_space_refine on Tue May 13 14:11:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6m_36008/05_2025/8j6m_36008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6m_36008/05_2025/8j6m_36008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6m_36008/05_2025/8j6m_36008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6m_36008/05_2025/8j6m_36008.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6m_36008/05_2025/8j6m_36008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6m_36008/05_2025/8j6m_36008.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.153 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 56 5.16 5 Na 1 4.78 5 C 7084 2.51 5 N 1644 2.21 5 O 1812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10599 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 641, 5156 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 641, 5156 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 5284 Chain: "A" Number of atoms: 5165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 641, 5156 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 641, 5156 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 5284 Chain: "B" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 134 Unusual residues: {' NA': 1, ' ZN': 1, 'CLR': 4, 'OLA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Unusual residues: {' ZN': 1, 'CLR': 4, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.09, per 1000 atoms: 1.05 Number of scatterers: 10599 At special positions: 0 Unit cell: (113.36, 86.32, 126.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 56 16.00 Na 1 11.00 O 1812 8.00 N 1644 7.00 C 7084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 782 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.04 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.07 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: 2.65 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 905 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 795 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 791 " 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 50.5% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 251 through 255 Proline residue: B 254 - end of helix No H-bonds generated for 'chain 'B' and resid 251 through 255' Processing helix chain 'B' and resid 302 through 338 removed outlier: 3.833A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 474 removed outlier: 4.509A pdb=" N TRP B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) Proline residue: B 458 - end of helix removed outlier: 3.605A pdb=" N THR B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.727A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.934A pdb=" N ILE B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.891A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 536 Processing helix chain 'B' and resid 542 through 563 Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.808A pdb=" N ASP B 574 " --> pdb=" O PHE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.851A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 622 removed outlier: 3.555A pdb=" N ALA B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 648 removed outlier: 3.583A pdb=" N THR B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 3.970A pdb=" N ASN B 694 " --> pdb=" O GLY B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 735 Processing helix chain 'B' and resid 740 through 762 Processing helix chain 'B' and resid 771 through 777 removed outlier: 3.514A pdb=" N GLU B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 812 removed outlier: 3.537A pdb=" N ALA B 799 " --> pdb=" O HIS B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 818 removed outlier: 3.693A pdb=" N ASP B 817 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 818 " --> pdb=" O ASP B 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Proline residue: A 254 - end of helix No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 302 through 338 removed outlier: 3.834A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 474 removed outlier: 4.504A pdb=" N TRP A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.603A pdb=" N THR A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.909A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 529 removed outlier: 3.777A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 Processing helix chain 'A' and resid 542 through 565 removed outlier: 4.139A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.803A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 622 removed outlier: 3.553A pdb=" N ALA A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 648 Processing helix chain 'A' and resid 683 through 705 removed outlier: 3.503A pdb=" N ASN A 694 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 735 Processing helix chain 'A' and resid 740 through 762 Processing helix chain 'A' and resid 771 through 777 removed outlier: 3.568A pdb=" N GLU A 777 " --> pdb=" O ALA A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 812 removed outlier: 3.537A pdb=" N ALA A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.502A pdb=" N ASP A 817 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 818 " --> pdb=" O ASP A 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 50 through 56 removed outlier: 4.390A pdb=" N HIS B 50 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B 163 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 77 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA4, first strand: chain 'B' and resid 170 through 171 removed outlier: 4.793A pdb=" N LYS B 192 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 181 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 56 removed outlier: 4.390A pdb=" N HIS A 50 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 163 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA A 77 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA8, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA9, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.794A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 176 through 181 634 hydrogen bonds defined for protein. 1822 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: 3.41 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1967 1.32 - 1.45: 3197 1.45 - 1.59: 5648 1.59 - 1.72: 0 1.72 - 1.85: 86 Bond restraints: 10898 Sorted by residual: bond pdb=" C TYR A 81 " pdb=" CA BTYR A 81 " ideal model delta sigma weight residual 1.521 1.422 0.099 1.19e-02 7.06e+03 6.96e+01 bond pdb=" C10 OLA A 906 " pdb=" C9 OLA A 906 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C10 OLA B 907 " pdb=" C9 OLA B 907 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" N TYR B 81 " pdb=" CA BTYR B 81 " ideal model delta sigma weight residual 1.456 1.409 0.048 1.21e-02 6.83e+03 1.55e+01 bond pdb=" CA VAL A 108 " pdb=" C VAL A 108 " ideal model delta sigma weight residual 1.525 1.557 -0.033 9.10e-03 1.21e+04 1.29e+01 ... (remaining 10893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 14191 2.39 - 4.79: 547 4.79 - 7.18: 96 7.18 - 9.58: 28 9.58 - 11.97: 6 Bond angle restraints: 14868 Sorted by residual: angle pdb=" N VAL A 534 " pdb=" CA VAL A 534 " pdb=" C VAL A 534 " ideal model delta sigma weight residual 110.53 119.47 -8.94 9.40e-01 1.13e+00 9.04e+01 angle pdb=" N SER A 274 " pdb=" CA SER A 274 " pdb=" C SER A 274 " ideal model delta sigma weight residual 111.28 121.07 -9.79 1.09e+00 8.42e-01 8.06e+01 angle pdb=" N VAL B 534 " pdb=" CA VAL B 534 " pdb=" C VAL B 534 " ideal model delta sigma weight residual 110.53 118.91 -8.38 9.40e-01 1.13e+00 7.95e+01 angle pdb=" N PHE B 275 " pdb=" CA PHE B 275 " pdb=" C PHE B 275 " ideal model delta sigma weight residual 110.19 119.77 -9.58 1.24e+00 6.50e-01 5.97e+01 angle pdb=" N LEU A 155 " pdb=" CA LEU A 155 " pdb=" C LEU A 155 " ideal model delta sigma weight residual 110.17 98.20 11.97 1.61e+00 3.86e-01 5.53e+01 ... (remaining 14863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.91: 6274 24.91 - 49.82: 410 49.82 - 74.73: 46 74.73 - 99.64: 17 99.64 - 124.55: 3 Dihedral angle restraints: 6750 sinusoidal: 2932 harmonic: 3818 Sorted by residual: dihedral pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " pdb=" SG CYS A 782 " pdb=" CB CYS A 782 " ideal model delta sinusoidal sigma weight residual 93.00 34.75 58.25 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS B 485 " pdb=" SG CYS B 485 " pdb=" SG CYS B 782 " pdb=" CB CYS B 782 " ideal model delta sinusoidal sigma weight residual 93.00 37.35 55.65 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA CYS A 782 " pdb=" C CYS A 782 " pdb=" N ILE A 783 " pdb=" CA ILE A 783 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 6747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1445 0.101 - 0.202: 196 0.202 - 0.303: 52 0.303 - 0.404: 12 0.404 - 0.506: 5 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CA PHE B 317 " pdb=" N PHE B 317 " pdb=" C PHE B 317 " pdb=" CB PHE B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CA PHE A 317 " pdb=" N PHE A 317 " pdb=" C PHE A 317 " pdb=" CB PHE A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CA ASN B 83 " pdb=" N ASN B 83 " pdb=" C ASN B 83 " pdb=" CB ASN B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 1707 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 906 " -0.279 2.00e-02 2.50e+03 2.13e-01 4.54e+02 pdb=" C11 OLA A 906 " 0.114 2.00e-02 2.50e+03 pdb=" C8 OLA A 906 " -0.115 2.00e-02 2.50e+03 pdb=" C9 OLA A 906 " 0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 907 " 0.279 2.00e-02 2.50e+03 2.13e-01 4.54e+02 pdb=" C11 OLA B 907 " -0.114 2.00e-02 2.50e+03 pdb=" C8 OLA B 907 " 0.114 2.00e-02 2.50e+03 pdb=" C9 OLA B 907 " -0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 525 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ALA B 525 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA B 525 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 526 " 0.020 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 28 2.47 - 3.07: 7058 3.07 - 3.68: 15994 3.68 - 4.29: 26004 4.29 - 4.90: 42374 Nonbonded interactions: 91458 Sorted by model distance: nonbonded pdb=" OD1 ASP B 574 " pdb="ZN ZN B 905 " model vdw 1.857 2.230 nonbonded pdb=" NE2 GLN B 100 " pdb=" O ASN A 90 " model vdw 2.291 3.120 nonbonded pdb=" OD1 ASP A 574 " pdb="ZN ZN A 901 " model vdw 2.292 2.230 nonbonded pdb=" NZ LYS B 732 " pdb=" OD1 ASP B 813 " model vdw 2.302 3.120 nonbonded pdb=" NZ LYS A 732 " pdb=" OD1 ASP A 813 " model vdw 2.302 3.120 ... (remaining 91453 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 80 or resid 82 through 827 or resid 902 through \ 904)) selection = (chain 'B' and (resid 44 through 80 or resid 82 through 827 or resid 902 through \ 904)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 34.190 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 0.009 0.226 10912 Z= 0.561 Angle : 1.110 11.972 14884 Z= 0.701 Chirality : 0.083 0.506 1710 Planarity : 0.009 0.213 1806 Dihedral : 16.073 124.552 4262 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 1.59 % Allowed : 16.96 % Favored : 81.45 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1268 helix: 1.31 (0.20), residues: 580 sheet: 1.50 (0.27), residues: 284 loop : -0.95 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 106 HIS 0.004 0.001 HIS A 636 PHE 0.023 0.002 PHE A 317 TYR 0.021 0.002 TYR B 605 ARG 0.007 0.001 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.19433 ( 634) hydrogen bonds : angle 7.38516 ( 1822) metal coordination : bond 0.16225 ( 6) SS BOND : bond 0.01515 ( 8) SS BOND : angle 3.71678 ( 16) covalent geometry : bond 0.00789 (10898) covalent geometry : angle 1.10424 (14868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.048 Fit side-chains REVERT: B 61 GLU cc_start: 0.8596 (tt0) cc_final: 0.8376 (tt0) REVERT: B 118 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6760 (mtp180) REVERT: B 123 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8288 (mm110) REVERT: B 302 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7401 (mmtt) REVERT: B 586 MET cc_start: 0.8307 (mtm) cc_final: 0.8098 (mtp) REVERT: B 684 MET cc_start: 0.5846 (tmt) cc_final: 0.5295 (mpp) REVERT: B 702 LEU cc_start: 0.7717 (tp) cc_final: 0.7302 (tt) REVERT: B 707 ARG cc_start: 0.7243 (tpp80) cc_final: 0.6898 (mmm160) REVERT: B 738 LYS cc_start: 0.7521 (mttt) cc_final: 0.7302 (mtpm) REVERT: A 61 GLU cc_start: 0.8588 (tt0) cc_final: 0.8357 (tt0) REVERT: A 118 ARG cc_start: 0.7207 (ttm-80) cc_final: 0.6685 (mtp180) REVERT: A 302 LYS cc_start: 0.8036 (mptm) cc_final: 0.7561 (mmtt) REVERT: A 505 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8235 (m) REVERT: A 684 MET cc_start: 0.5580 (tmt) cc_final: 0.5113 (mpp) REVERT: A 707 ARG cc_start: 0.7280 (tpp80) cc_final: 0.6963 (mmm160) REVERT: A 774 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7634 (mt-10) outliers start: 18 outliers final: 9 residues processed: 203 average time/residue: 0.9893 time to fit residues: 219.7558 Evaluate side-chains 168 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 764 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 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 461 GLN B 720 ASN A 461 GLN A 475 ASN A 541 HIS A 646 GLN A 694 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120311 restraints weight = 20601.931| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.10 r_work: 0.3089 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10912 Z= 0.173 Angle : 0.610 7.245 14884 Z= 0.312 Chirality : 0.045 0.190 1710 Planarity : 0.004 0.035 1806 Dihedral : 8.469 55.936 1964 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.00 % Allowed : 18.29 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1268 helix: 2.23 (0.19), residues: 584 sheet: 1.33 (0.28), residues: 284 loop : -0.83 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.005 0.001 HIS B 563 PHE 0.023 0.002 PHE A 317 TYR 0.015 0.002 TYR A 605 ARG 0.006 0.001 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.05089 ( 634) hydrogen bonds : angle 4.96581 ( 1822) metal coordination : bond 0.01074 ( 6) SS BOND : bond 0.00217 ( 8) SS BOND : angle 2.13335 ( 16) covalent geometry : bond 0.00396 (10898) covalent geometry : angle 0.60629 (14868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.159 Fit side-chains REVERT: B 61 GLU cc_start: 0.8297 (tt0) cc_final: 0.8057 (tt0) REVERT: B 90 ASN cc_start: 0.7839 (m-40) cc_final: 0.7622 (m-40) REVERT: B 118 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6689 (mtp180) REVERT: B 158 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: B 274 SER cc_start: 0.7439 (m) cc_final: 0.7197 (t) REVERT: B 536 TYR cc_start: 0.7351 (m-80) cc_final: 0.7135 (m-80) REVERT: B 576 SER cc_start: 0.8317 (m) cc_final: 0.7993 (p) REVERT: B 684 MET cc_start: 0.5726 (tmt) cc_final: 0.4975 (mpm) REVERT: B 702 LEU cc_start: 0.7552 (tp) cc_final: 0.7187 (tt) REVERT: B 707 ARG cc_start: 0.7177 (tpp80) cc_final: 0.6770 (mmm160) REVERT: B 738 LYS cc_start: 0.7610 (mttt) cc_final: 0.7162 (mtpm) REVERT: A 118 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.6547 (mtp180) REVERT: A 158 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: A 302 LYS cc_start: 0.7891 (mptm) cc_final: 0.7596 (mmtm) REVERT: A 536 TYR cc_start: 0.7460 (m-80) cc_final: 0.7150 (m-80) REVERT: A 576 SER cc_start: 0.8294 (m) cc_final: 0.7987 (p) REVERT: A 684 MET cc_start: 0.5486 (tmt) cc_final: 0.4836 (mpp) REVERT: A 692 LEU cc_start: 0.7189 (mp) cc_final: 0.6954 (mp) REVERT: A 707 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6730 (mmm160) REVERT: A 738 LYS cc_start: 0.6913 (mtpm) cc_final: 0.5703 (mmtp) REVERT: A 774 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7743 (mt-10) outliers start: 34 outliers final: 18 residues processed: 192 average time/residue: 0.8869 time to fit residues: 188.1309 Evaluate side-chains 179 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 713 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 475 ASN B 720 ASN B 779 ASN A 646 GLN A 764 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118466 restraints weight = 18976.602| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.87 r_work: 0.3088 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10912 Z= 0.185 Angle : 0.574 7.501 14884 Z= 0.296 Chirality : 0.044 0.145 1710 Planarity : 0.004 0.037 1806 Dihedral : 7.394 57.208 1956 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.36 % Allowed : 18.99 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1268 helix: 2.37 (0.20), residues: 584 sheet: 1.15 (0.29), residues: 284 loop : -0.81 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 106 HIS 0.005 0.001 HIS A 563 PHE 0.016 0.002 PHE A 317 TYR 0.021 0.002 TYR A 605 ARG 0.005 0.001 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04903 ( 634) hydrogen bonds : angle 4.72455 ( 1822) metal coordination : bond 0.00772 ( 6) SS BOND : bond 0.00247 ( 8) SS BOND : angle 2.11751 ( 16) covalent geometry : bond 0.00439 (10898) covalent geometry : angle 0.56971 (14868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.052 Fit side-chains REVERT: B 118 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.6629 (mtp180) REVERT: B 172 ARG cc_start: 0.8300 (mpt180) cc_final: 0.8053 (mmt-90) REVERT: B 207 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: B 274 SER cc_start: 0.7354 (OUTLIER) cc_final: 0.7105 (t) REVERT: B 297 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8506 (mm) REVERT: B 576 SER cc_start: 0.8548 (m) cc_final: 0.8166 (p) REVERT: B 684 MET cc_start: 0.5680 (tmt) cc_final: 0.5225 (mpp) REVERT: B 702 LEU cc_start: 0.7676 (tp) cc_final: 0.7332 (tt) REVERT: B 707 ARG cc_start: 0.7328 (tpp80) cc_final: 0.6922 (mmm160) REVERT: B 738 LYS cc_start: 0.7823 (mttt) cc_final: 0.7380 (mtmm) REVERT: B 753 MET cc_start: 0.8788 (mmt) cc_final: 0.8118 (mmt) REVERT: A 118 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.6510 (mtp180) REVERT: A 158 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8353 (mt0) REVERT: A 207 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 297 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 302 LYS cc_start: 0.7918 (mptm) cc_final: 0.7626 (mmmm) REVERT: A 536 TYR cc_start: 0.7530 (m-80) cc_final: 0.7234 (m-80) REVERT: A 576 SER cc_start: 0.8477 (m) cc_final: 0.8110 (p) REVERT: A 684 MET cc_start: 0.5586 (tmt) cc_final: 0.5083 (mpm) REVERT: A 692 LEU cc_start: 0.7381 (mp) cc_final: 0.7156 (mp) REVERT: A 707 ARG cc_start: 0.7341 (tpp80) cc_final: 0.6908 (mmm160) REVERT: A 738 LYS cc_start: 0.7130 (mtpm) cc_final: 0.6266 (mtmm) REVERT: A 774 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7948 (mt-10) outliers start: 38 outliers final: 22 residues processed: 188 average time/residue: 0.8536 time to fit residues: 177.9398 Evaluate side-chains 188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN B 720 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.152957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120792 restraints weight = 22838.428| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.39 r_work: 0.3036 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10912 Z= 0.149 Angle : 0.520 7.159 14884 Z= 0.268 Chirality : 0.042 0.143 1710 Planarity : 0.003 0.037 1806 Dihedral : 7.161 59.204 1956 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.36 % Allowed : 19.08 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1268 helix: 2.54 (0.20), residues: 584 sheet: 1.11 (0.29), residues: 284 loop : -0.75 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.004 0.001 HIS A 487 PHE 0.013 0.001 PHE A 317 TYR 0.023 0.002 TYR A 605 ARG 0.004 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 634) hydrogen bonds : angle 4.56002 ( 1822) metal coordination : bond 0.00680 ( 6) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.82281 ( 16) covalent geometry : bond 0.00348 (10898) covalent geometry : angle 0.51715 (14868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 1.065 Fit side-chains REVERT: B 118 ARG cc_start: 0.7228 (ttm-80) cc_final: 0.6506 (mtp180) REVERT: B 158 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: B 207 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: B 274 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.7060 (t) REVERT: B 297 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (mm) REVERT: B 576 SER cc_start: 0.8439 (m) cc_final: 0.8072 (p) REVERT: B 684 MET cc_start: 0.5522 (tmt) cc_final: 0.5099 (mpm) REVERT: B 702 LEU cc_start: 0.7588 (tp) cc_final: 0.7269 (tt) REVERT: B 707 ARG cc_start: 0.7259 (tpp80) cc_final: 0.6792 (mmm160) REVERT: B 738 LYS cc_start: 0.7524 (mttt) cc_final: 0.7002 (mtmm) REVERT: B 753 MET cc_start: 0.8631 (mmt) cc_final: 0.7977 (mmt) REVERT: A 83 ASN cc_start: 0.8281 (p0) cc_final: 0.7994 (p0) REVERT: A 118 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6355 (mtp180) REVERT: A 207 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 297 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 524 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6362 (mtt180) REVERT: A 536 TYR cc_start: 0.7563 (m-80) cc_final: 0.7297 (m-80) REVERT: A 576 SER cc_start: 0.8545 (m) cc_final: 0.8143 (p) REVERT: A 684 MET cc_start: 0.5433 (tmt) cc_final: 0.4993 (mpm) REVERT: A 692 LEU cc_start: 0.7166 (mp) cc_final: 0.6921 (mm) REVERT: A 707 ARG cc_start: 0.7264 (tpp80) cc_final: 0.6802 (mmm160) REVERT: A 713 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: A 738 LYS cc_start: 0.7006 (mtpm) cc_final: 0.6146 (mtmm) REVERT: A 774 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7711 (mt-10) outliers start: 38 outliers final: 20 residues processed: 185 average time/residue: 0.9238 time to fit residues: 188.0696 Evaluate side-chains 180 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS B 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.150937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116671 restraints weight = 17729.414| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.47 r_work: 0.3101 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10912 Z= 0.197 Angle : 0.568 8.387 14884 Z= 0.291 Chirality : 0.044 0.144 1710 Planarity : 0.004 0.037 1806 Dihedral : 7.207 59.970 1952 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.06 % Allowed : 19.35 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1268 helix: 2.44 (0.20), residues: 584 sheet: 1.17 (0.30), residues: 272 loop : -0.87 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 629 HIS 0.005 0.001 HIS A 563 PHE 0.012 0.002 PHE B 632 TYR 0.028 0.002 TYR A 605 ARG 0.006 0.001 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 634) hydrogen bonds : angle 4.63078 ( 1822) metal coordination : bond 0.00771 ( 6) SS BOND : bond 0.00312 ( 8) SS BOND : angle 2.15985 ( 16) covalent geometry : bond 0.00474 (10898) covalent geometry : angle 0.56391 (14868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 1.073 Fit side-chains REVERT: B 118 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6511 (mtp180) REVERT: B 158 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: B 207 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: B 274 SER cc_start: 0.7230 (OUTLIER) cc_final: 0.7011 (t) REVERT: B 297 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8467 (mm) REVERT: B 519 ASP cc_start: 0.7114 (t0) cc_final: 0.6784 (t70) REVERT: B 576 SER cc_start: 0.8466 (m) cc_final: 0.8040 (p) REVERT: B 684 MET cc_start: 0.5668 (tmt) cc_final: 0.5205 (mpm) REVERT: B 707 ARG cc_start: 0.7333 (tpp80) cc_final: 0.6817 (mmm160) REVERT: B 738 LYS cc_start: 0.7568 (mttt) cc_final: 0.7040 (mtmm) REVERT: A 118 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6391 (mtp180) REVERT: A 158 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: A 207 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 297 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 524 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6447 (mtt180) REVERT: A 536 TYR cc_start: 0.7619 (m-80) cc_final: 0.7381 (m-80) REVERT: A 576 SER cc_start: 0.8461 (m) cc_final: 0.8030 (p) REVERT: A 684 MET cc_start: 0.5567 (tmt) cc_final: 0.5043 (mpm) REVERT: A 692 LEU cc_start: 0.7182 (mp) cc_final: 0.6890 (mm) REVERT: A 707 ARG cc_start: 0.7352 (tpp80) cc_final: 0.6820 (mmm160) REVERT: A 713 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8093 (mmm) REVERT: A 774 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7866 (mt-10) outliers start: 46 outliers final: 28 residues processed: 180 average time/residue: 0.9257 time to fit residues: 183.5577 Evaluate side-chains 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 0.0000 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.153248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119821 restraints weight = 14146.548| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.93 r_work: 0.3160 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10912 Z= 0.127 Angle : 0.501 7.124 14884 Z= 0.258 Chirality : 0.041 0.142 1710 Planarity : 0.003 0.037 1806 Dihedral : 6.998 59.224 1952 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.89 % Allowed : 19.96 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.23), residues: 1268 helix: 2.65 (0.20), residues: 584 sheet: 1.00 (0.30), residues: 284 loop : -0.70 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.004 0.001 HIS A 563 PHE 0.011 0.001 PHE A 317 TYR 0.027 0.001 TYR A 605 ARG 0.005 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 634) hydrogen bonds : angle 4.49003 ( 1822) metal coordination : bond 0.00632 ( 6) SS BOND : bond 0.00322 ( 8) SS BOND : angle 1.71012 ( 16) covalent geometry : bond 0.00293 (10898) covalent geometry : angle 0.49771 (14868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.056 Fit side-chains REVERT: B 101 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7412 (mppt) REVERT: B 118 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6521 (mtp180) REVERT: B 158 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: B 207 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: B 297 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8413 (mm) REVERT: B 570 ASN cc_start: 0.7199 (m-40) cc_final: 0.6858 (m110) REVERT: B 576 SER cc_start: 0.8454 (m) cc_final: 0.8042 (p) REVERT: B 577 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: B 684 MET cc_start: 0.5737 (tmt) cc_final: 0.5317 (mpm) REVERT: B 702 LEU cc_start: 0.7625 (tp) cc_final: 0.7268 (tt) REVERT: B 707 ARG cc_start: 0.7333 (tpp80) cc_final: 0.6832 (mmm160) REVERT: B 713 MET cc_start: 0.8144 (mmm) cc_final: 0.7881 (mtp) REVERT: B 738 LYS cc_start: 0.7540 (mttt) cc_final: 0.6739 (mtmm) REVERT: B 753 MET cc_start: 0.8681 (mmt) cc_final: 0.8087 (mmt) REVERT: B 815 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6680 (p0) REVERT: A 83 ASN cc_start: 0.8335 (p0) cc_final: 0.8022 (p0) REVERT: A 118 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6400 (mtp180) REVERT: A 207 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: A 297 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 536 TYR cc_start: 0.7620 (m-80) cc_final: 0.7366 (m-80) REVERT: A 576 SER cc_start: 0.8585 (m) cc_final: 0.8154 (p) REVERT: A 684 MET cc_start: 0.5629 (tmt) cc_final: 0.5109 (mpm) REVERT: A 692 LEU cc_start: 0.7192 (mp) cc_final: 0.6977 (mm) REVERT: A 707 ARG cc_start: 0.7364 (tpp80) cc_final: 0.6864 (mmm160) REVERT: A 713 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8102 (mmm) REVERT: A 753 MET cc_start: 0.8659 (mmt) cc_final: 0.8020 (mmt) REVERT: A 774 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7840 (mt-10) outliers start: 44 outliers final: 23 residues processed: 183 average time/residue: 0.8835 time to fit residues: 178.5532 Evaluate side-chains 183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 815 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 101 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 17 optimal weight: 0.0020 overall best weight: 0.6708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121460 restraints weight = 22985.596| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.56 r_work: 0.3068 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10912 Z= 0.136 Angle : 0.503 7.160 14884 Z= 0.258 Chirality : 0.041 0.141 1710 Planarity : 0.003 0.037 1806 Dihedral : 6.914 59.256 1952 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.62 % Allowed : 20.23 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.23), residues: 1268 helix: 2.68 (0.20), residues: 584 sheet: 1.15 (0.30), residues: 272 loop : -0.70 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS A 563 PHE 0.011 0.001 PHE B 317 TYR 0.031 0.002 TYR A 605 ARG 0.006 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 634) hydrogen bonds : angle 4.45633 ( 1822) metal coordination : bond 0.00640 ( 6) SS BOND : bond 0.00209 ( 8) SS BOND : angle 1.65142 ( 16) covalent geometry : bond 0.00321 (10898) covalent geometry : angle 0.50083 (14868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.063 Fit side-chains REVERT: B 101 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7578 (mppt) REVERT: B 118 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.6584 (mtp180) REVERT: B 152 MET cc_start: 0.8521 (mtt) cc_final: 0.8185 (mtt) REVERT: B 158 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: B 207 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 294 GLU cc_start: 0.8671 (tt0) cc_final: 0.8405 (tm-30) REVERT: B 297 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8448 (mm) REVERT: B 570 ASN cc_start: 0.7239 (m-40) cc_final: 0.6900 (m110) REVERT: B 576 SER cc_start: 0.8456 (m) cc_final: 0.8023 (p) REVERT: B 577 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: B 684 MET cc_start: 0.5795 (tmt) cc_final: 0.5343 (mpm) REVERT: B 702 LEU cc_start: 0.7649 (tp) cc_final: 0.7290 (tt) REVERT: B 707 ARG cc_start: 0.7330 (tpp80) cc_final: 0.6868 (mmm160) REVERT: B 738 LYS cc_start: 0.7548 (mttt) cc_final: 0.6739 (mtmm) REVERT: B 753 MET cc_start: 0.8716 (mmt) cc_final: 0.8123 (mmt) REVERT: B 815 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6730 (p0) REVERT: A 83 ASN cc_start: 0.8235 (p0) cc_final: 0.7918 (p0) REVERT: A 118 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6487 (mtp180) REVERT: A 158 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: A 207 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: A 297 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8422 (mm) REVERT: A 536 TYR cc_start: 0.7661 (m-80) cc_final: 0.7402 (m-80) REVERT: A 576 SER cc_start: 0.8598 (m) cc_final: 0.8175 (p) REVERT: A 684 MET cc_start: 0.5612 (tmt) cc_final: 0.5187 (mpm) REVERT: A 692 LEU cc_start: 0.7213 (mp) cc_final: 0.7000 (mm) REVERT: A 707 ARG cc_start: 0.7343 (tpp80) cc_final: 0.6876 (mmm160) REVERT: A 713 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8170 (mmm) REVERT: A 753 MET cc_start: 0.8696 (mmt) cc_final: 0.8079 (mmt) REVERT: A 774 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7834 (mt-10) outliers start: 41 outliers final: 27 residues processed: 180 average time/residue: 0.8741 time to fit residues: 174.4197 Evaluate side-chains 191 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 815 ASP Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN A 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117859 restraints weight = 15358.849| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.99 r_work: 0.3127 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10912 Z= 0.177 Angle : 0.543 7.366 14884 Z= 0.278 Chirality : 0.043 0.142 1710 Planarity : 0.003 0.037 1806 Dihedral : 6.978 59.057 1951 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.53 % Allowed : 20.23 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1268 helix: 2.57 (0.20), residues: 584 sheet: 1.14 (0.30), residues: 272 loop : -0.76 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 629 HIS 0.005 0.001 HIS A 487 PHE 0.012 0.002 PHE B 632 TYR 0.045 0.002 TYR B 605 ARG 0.004 0.001 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 634) hydrogen bonds : angle 4.51940 ( 1822) metal coordination : bond 0.00724 ( 6) SS BOND : bond 0.00277 ( 8) SS BOND : angle 1.93691 ( 16) covalent geometry : bond 0.00427 (10898) covalent geometry : angle 0.53935 (14868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.148 Fit side-chains REVERT: B 101 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7596 (mppt) REVERT: B 118 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.6474 (mtp180) REVERT: B 152 MET cc_start: 0.8513 (mtt) cc_final: 0.8087 (mtt) REVERT: B 158 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: B 207 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: B 297 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8380 (mm) REVERT: B 519 ASP cc_start: 0.6928 (t0) cc_final: 0.6677 (t70) REVERT: B 554 MET cc_start: 0.8273 (mmp) cc_final: 0.8062 (mmm) REVERT: B 576 SER cc_start: 0.8462 (m) cc_final: 0.8012 (p) REVERT: B 684 MET cc_start: 0.5820 (tmt) cc_final: 0.5319 (mpm) REVERT: B 702 LEU cc_start: 0.7631 (tp) cc_final: 0.7303 (tt) REVERT: B 707 ARG cc_start: 0.7337 (tpp80) cc_final: 0.6815 (mmm160) REVERT: B 738 LYS cc_start: 0.7541 (mttt) cc_final: 0.6960 (mtmm) REVERT: B 753 MET cc_start: 0.8657 (mmt) cc_final: 0.8001 (mmt) REVERT: A 83 ASN cc_start: 0.8431 (p0) cc_final: 0.8156 (p0) REVERT: A 118 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.6344 (mtp180) REVERT: A 158 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: A 207 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: A 297 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 536 TYR cc_start: 0.7661 (m-80) cc_final: 0.7387 (m-80) REVERT: A 576 SER cc_start: 0.8595 (m) cc_final: 0.8129 (p) REVERT: A 684 MET cc_start: 0.5885 (tmt) cc_final: 0.5374 (mpm) REVERT: A 692 LEU cc_start: 0.7146 (mp) cc_final: 0.6932 (mm) REVERT: A 707 ARG cc_start: 0.7340 (tpp80) cc_final: 0.6812 (mmm160) REVERT: A 713 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: A 753 MET cc_start: 0.8640 (mmt) cc_final: 0.7976 (mmt) REVERT: A 774 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7862 (mt-10) outliers start: 40 outliers final: 29 residues processed: 173 average time/residue: 0.8906 time to fit residues: 170.2218 Evaluate side-chains 187 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 0.0470 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 ASN B 646 GLN A 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119918 restraints weight = 22138.506| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.35 r_work: 0.3058 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10912 Z= 0.144 Angle : 0.510 6.976 14884 Z= 0.262 Chirality : 0.042 0.141 1710 Planarity : 0.003 0.038 1806 Dihedral : 6.891 58.415 1951 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.62 % Allowed : 20.05 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1268 helix: 2.65 (0.20), residues: 584 sheet: 1.14 (0.30), residues: 272 loop : -0.71 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.004 0.001 HIS A 487 PHE 0.011 0.001 PHE B 632 TYR 0.031 0.002 TYR A 605 ARG 0.005 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 634) hydrogen bonds : angle 4.47437 ( 1822) metal coordination : bond 0.00658 ( 6) SS BOND : bond 0.00241 ( 8) SS BOND : angle 1.73684 ( 16) covalent geometry : bond 0.00342 (10898) covalent geometry : angle 0.50703 (14868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.175 Fit side-chains REVERT: B 100 GLN cc_start: 0.8380 (tt0) cc_final: 0.7909 (tm-30) REVERT: B 101 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7516 (mppt) REVERT: B 118 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.6509 (mtp180) REVERT: B 158 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: B 207 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: B 297 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 554 MET cc_start: 0.8215 (mmp) cc_final: 0.7998 (mmm) REVERT: B 576 SER cc_start: 0.8415 (m) cc_final: 0.7964 (p) REVERT: B 577 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: B 684 MET cc_start: 0.5754 (tmt) cc_final: 0.5289 (mpm) REVERT: B 702 LEU cc_start: 0.7595 (tp) cc_final: 0.7270 (tt) REVERT: B 707 ARG cc_start: 0.7300 (tpp80) cc_final: 0.6806 (mmm160) REVERT: B 713 MET cc_start: 0.8063 (mmm) cc_final: 0.7825 (mtp) REVERT: B 720 ASN cc_start: 0.7983 (m110) cc_final: 0.7695 (m110) REVERT: B 738 LYS cc_start: 0.7408 (mttt) cc_final: 0.6935 (mtmm) REVERT: B 753 MET cc_start: 0.8641 (mmt) cc_final: 0.8004 (mmt) REVERT: A 83 ASN cc_start: 0.8258 (p0) cc_final: 0.7963 (p0) REVERT: A 118 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6402 (mtp180) REVERT: A 158 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: A 207 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 297 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8443 (mm) REVERT: A 536 TYR cc_start: 0.7631 (m-80) cc_final: 0.7355 (m-80) REVERT: A 576 SER cc_start: 0.8550 (m) cc_final: 0.8087 (p) REVERT: A 684 MET cc_start: 0.5813 (tmt) cc_final: 0.5372 (mpm) REVERT: A 692 LEU cc_start: 0.7057 (mp) cc_final: 0.6847 (mm) REVERT: A 707 ARG cc_start: 0.7288 (tpp80) cc_final: 0.6792 (mmm160) REVERT: A 713 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8022 (mmm) REVERT: A 753 MET cc_start: 0.8649 (mmt) cc_final: 0.8024 (mmt) REVERT: A 774 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7753 (mt-10) outliers start: 41 outliers final: 31 residues processed: 177 average time/residue: 0.9314 time to fit residues: 181.7844 Evaluate side-chains 192 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 764 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN A 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118627 restraints weight = 18847.469| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.87 r_work: 0.3080 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10912 Z= 0.178 Angle : 0.539 7.064 14884 Z= 0.277 Chirality : 0.043 0.141 1710 Planarity : 0.003 0.038 1806 Dihedral : 6.946 58.487 1951 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.53 % Allowed : 20.14 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1268 helix: 2.59 (0.20), residues: 584 sheet: 1.15 (0.30), residues: 272 loop : -0.75 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 629 HIS 0.005 0.001 HIS A 563 PHE 0.011 0.002 PHE B 632 TYR 0.044 0.002 TYR B 605 ARG 0.004 0.001 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 634) hydrogen bonds : angle 4.51789 ( 1822) metal coordination : bond 0.00718 ( 6) SS BOND : bond 0.00277 ( 8) SS BOND : angle 1.92377 ( 16) covalent geometry : bond 0.00429 (10898) covalent geometry : angle 0.53597 (14868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.009 Fit side-chains REVERT: B 100 GLN cc_start: 0.8467 (tt0) cc_final: 0.8103 (tm-30) REVERT: B 101 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7628 (mppt) REVERT: B 118 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.6459 (mtp180) REVERT: B 158 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: B 207 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: B 297 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8411 (mm) REVERT: B 519 ASP cc_start: 0.7083 (t0) cc_final: 0.6842 (t70) REVERT: B 554 MET cc_start: 0.8377 (mmp) cc_final: 0.8164 (mmm) REVERT: B 576 SER cc_start: 0.8500 (m) cc_final: 0.8047 (p) REVERT: B 577 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: B 684 MET cc_start: 0.5896 (tmt) cc_final: 0.5324 (mpm) REVERT: B 702 LEU cc_start: 0.7594 (tp) cc_final: 0.7264 (tt) REVERT: B 707 ARG cc_start: 0.7378 (tpp80) cc_final: 0.6824 (mmm160) REVERT: B 720 ASN cc_start: 0.8124 (m110) cc_final: 0.7842 (m110) REVERT: B 738 LYS cc_start: 0.7518 (mttt) cc_final: 0.7003 (mtmm) REVERT: B 753 MET cc_start: 0.8698 (mmt) cc_final: 0.8080 (mmt) REVERT: A 83 ASN cc_start: 0.8497 (p0) cc_final: 0.8229 (p0) REVERT: A 118 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.6429 (mtp180) REVERT: A 158 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: A 207 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 297 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8526 (mm) REVERT: A 536 TYR cc_start: 0.7714 (m-80) cc_final: 0.7506 (m-80) REVERT: A 576 SER cc_start: 0.8628 (m) cc_final: 0.8162 (p) REVERT: A 684 MET cc_start: 0.5945 (tmt) cc_final: 0.5390 (mpm) REVERT: A 692 LEU cc_start: 0.7158 (mp) cc_final: 0.6946 (mm) REVERT: A 707 ARG cc_start: 0.7416 (tpp80) cc_final: 0.6854 (mmm160) REVERT: A 713 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8159 (mmm) REVERT: A 753 MET cc_start: 0.8651 (mmt) cc_final: 0.8073 (mmt) REVERT: A 774 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7932 (mt-10) outliers start: 40 outliers final: 28 residues processed: 175 average time/residue: 0.9241 time to fit residues: 177.7647 Evaluate side-chains 188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN A 636 HIS A 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121074 restraints weight = 27727.866| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.24 r_work: 0.3024 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10912 Z= 0.142 Angle : 0.509 6.890 14884 Z= 0.262 Chirality : 0.042 0.140 1710 Planarity : 0.003 0.037 1806 Dihedral : 6.876 57.979 1951 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.62 % Allowed : 20.14 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1268 helix: 2.68 (0.20), residues: 584 sheet: 1.17 (0.30), residues: 272 loop : -0.69 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.004 0.001 HIS A 563 PHE 0.011 0.001 PHE B 317 TYR 0.038 0.002 TYR B 605 ARG 0.005 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 634) hydrogen bonds : angle 4.47047 ( 1822) metal coordination : bond 0.00658 ( 6) SS BOND : bond 0.00234 ( 8) SS BOND : angle 1.68232 ( 16) covalent geometry : bond 0.00338 (10898) covalent geometry : angle 0.50662 (14868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7807.59 seconds wall clock time: 135 minutes 6.85 seconds (8106.85 seconds total)