Starting phenix.real_space_refine on Mon Jul 28 19:27:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6m_36008/07_2025/8j6m_36008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6m_36008/07_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_36008/07_2025/8j6m_36008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6m_36008/07_2025/8j6m_36008.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6m_36008/07_2025/8j6m_36008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6m_36008/07_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-5711/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: 12.21, per 1000 atoms: 1.15 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: 2.58 Conformation dependent library (CDL) restraints added in 2.7 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: 1.08 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: 3.73 Time building geometry restraints manager: 3.11 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 37.350 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.630 ------------------------------------------------------------------------------- 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 : 0.989 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: 1.0250 time to fit residues: 227.6523 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 : 1.059 ------------------------------------------------------------------------------- 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 = 0.120309 restraints weight = 20602.328| |-----------------------------------------------------------------------------| 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: 0.7605 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 7.244 14884 Z= 0.312 Chirality : 0.045 0.190 1710 Planarity : 0.004 0.035 1806 Dihedral : 8.469 55.937 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 2.13334 ( 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 : 1.080 Fit side-chains REVERT: B 61 GLU cc_start: 0.8297 (tt0) cc_final: 0.8058 (tt0) REVERT: B 90 ASN cc_start: 0.7845 (m-40) cc_final: 0.7628 (m-40) REVERT: B 118 ARG cc_start: 0.7311 (ttm-80) cc_final: 0.6677 (mtp180) REVERT: B 158 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: B 274 SER cc_start: 0.7435 (m) cc_final: 0.7193 (t) REVERT: B 536 TYR cc_start: 0.7350 (m-80) cc_final: 0.7135 (m-80) REVERT: B 576 SER cc_start: 0.8318 (m) cc_final: 0.7993 (p) REVERT: B 684 MET cc_start: 0.5723 (tmt) cc_final: 0.4974 (mpm) REVERT: B 702 LEU cc_start: 0.7555 (tp) cc_final: 0.7189 (tt) REVERT: B 707 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6774 (mmm160) REVERT: B 738 LYS cc_start: 0.7611 (mttt) cc_final: 0.7162 (mtpm) REVERT: A 118 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.6536 (mtp180) REVERT: A 158 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: A 302 LYS cc_start: 0.7888 (mptm) cc_final: 0.7592 (mmtm) REVERT: A 536 TYR cc_start: 0.7462 (m-80) cc_final: 0.7152 (m-80) REVERT: A 576 SER cc_start: 0.8294 (m) cc_final: 0.7986 (p) REVERT: A 684 MET cc_start: 0.5480 (tmt) cc_final: 0.4832 (mpp) REVERT: A 692 LEU cc_start: 0.7208 (mp) cc_final: 0.6972 (mp) REVERT: A 707 ARG cc_start: 0.7185 (tpp80) cc_final: 0.6733 (mmm160) REVERT: A 738 LYS cc_start: 0.6915 (mtpm) cc_final: 0.5705 (mmtp) REVERT: A 774 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7743 (mt-10) outliers start: 34 outliers final: 18 residues processed: 192 average time/residue: 0.9200 time to fit residues: 194.5912 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 : 1.050 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 0.9990 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: 5.9990 chunk 100 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.152343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118357 restraints weight = 18903.395| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.79 r_work: 0.3080 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 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 = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10912 Z= 0.190 Angle : 0.575 7.266 14884 Z= 0.297 Chirality : 0.044 0.144 1710 Planarity : 0.004 0.037 1806 Dihedral : 7.425 57.171 1956 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.53 % Allowed : 18.73 % Favored : 77.74 % 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: 1.69 (0.22), residues: 1268 helix: 2.35 (0.20), residues: 584 sheet: 1.16 (0.29), residues: 284 loop : -0.82 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 629 HIS 0.004 0.001 HIS A 563 PHE 0.016 0.002 PHE A 317 TYR 0.018 0.002 TYR A 605 ARG 0.005 0.001 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 634) hydrogen bonds : angle 4.75698 ( 1822) metal coordination : bond 0.00797 ( 6) SS BOND : bond 0.00411 ( 8) SS BOND : angle 2.09020 ( 16) covalent geometry : bond 0.00453 (10898) covalent geometry : angle 0.57093 (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 202 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.069 Fit side-chains REVERT: B 118 ARG cc_start: 0.7314 (ttm-80) cc_final: 0.6583 (mtp180) REVERT: B 158 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: B 274 SER cc_start: 0.7267 (OUTLIER) cc_final: 0.7011 (t) REVERT: B 297 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8483 (mm) REVERT: B 536 TYR cc_start: 0.7385 (m-80) cc_final: 0.7175 (m-80) REVERT: B 576 SER cc_start: 0.8516 (m) cc_final: 0.8128 (p) REVERT: B 684 MET cc_start: 0.5638 (tmt) cc_final: 0.5134 (mpm) REVERT: B 702 LEU cc_start: 0.7581 (tp) cc_final: 0.7255 (tt) REVERT: B 707 ARG cc_start: 0.7272 (tpp80) cc_final: 0.6847 (mmm160) REVERT: B 738 LYS cc_start: 0.7749 (mttt) cc_final: 0.7300 (mtpm) REVERT: A 118 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.6461 (mtp180) REVERT: A 158 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8330 (mt0) REVERT: A 207 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: A 297 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 302 LYS cc_start: 0.7783 (mptm) cc_final: 0.7518 (mmmm) REVERT: A 536 TYR cc_start: 0.7452 (m-80) cc_final: 0.7150 (m-80) REVERT: A 576 SER cc_start: 0.8438 (m) cc_final: 0.8056 (p) REVERT: A 684 MET cc_start: 0.5552 (tmt) cc_final: 0.5048 (mpm) REVERT: A 692 LEU cc_start: 0.7248 (mp) cc_final: 0.7023 (mp) REVERT: A 707 ARG cc_start: 0.7289 (tpp80) cc_final: 0.6837 (mmm160) REVERT: A 774 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7942 (mt-10) outliers start: 40 outliers final: 24 residues processed: 187 average time/residue: 0.8887 time to fit residues: 184.1092 Evaluate side-chains 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 B 779 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118973 restraints weight = 22813.568| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.41 r_work: 0.3055 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10912 Z= 0.190 Angle : 0.565 7.475 14884 Z= 0.290 Chirality : 0.044 0.145 1710 Planarity : 0.004 0.038 1806 Dihedral : 7.314 59.324 1956 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.80 % Allowed : 18.82 % Favored : 77.39 % 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: 1.68 (0.23), residues: 1268 helix: 2.38 (0.20), residues: 584 sheet: 1.07 (0.29), residues: 284 loop : -0.82 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 629 HIS 0.006 0.001 HIS B 563 PHE 0.013 0.002 PHE B 317 TYR 0.024 0.002 TYR A 605 ARG 0.004 0.001 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 634) hydrogen bonds : angle 4.66456 ( 1822) metal coordination : bond 0.00773 ( 6) SS BOND : bond 0.00255 ( 8) SS BOND : angle 2.07488 ( 16) covalent geometry : bond 0.00457 (10898) covalent geometry : angle 0.56163 (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 201 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 1.124 Fit side-chains REVERT: B 118 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.6566 (mtp180) REVERT: B 172 ARG cc_start: 0.8310 (mpt180) cc_final: 0.8034 (mmt-90) REVERT: B 207 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: B 274 SER cc_start: 0.7307 (OUTLIER) cc_final: 0.7073 (t) REVERT: B 297 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8481 (mm) REVERT: B 576 SER cc_start: 0.8478 (m) cc_final: 0.8080 (p) REVERT: B 684 MET cc_start: 0.5549 (tmt) cc_final: 0.5123 (mpm) REVERT: B 702 LEU cc_start: 0.7600 (tp) cc_final: 0.7280 (tt) REVERT: B 707 ARG cc_start: 0.7295 (tpp80) cc_final: 0.6828 (mmm160) REVERT: B 738 LYS cc_start: 0.7735 (mttt) cc_final: 0.7228 (mtmm) REVERT: B 753 MET cc_start: 0.8695 (mmt) cc_final: 0.8035 (mmt) REVERT: A 118 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6427 (mtp180) REVERT: A 207 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: A 297 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8418 (mm) REVERT: A 524 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6406 (mtt180) REVERT: A 536 TYR cc_start: 0.7549 (m-80) cc_final: 0.7298 (m-80) REVERT: A 576 SER cc_start: 0.8403 (m) cc_final: 0.8010 (p) REVERT: A 684 MET cc_start: 0.5459 (tmt) cc_final: 0.5015 (mpm) REVERT: A 692 LEU cc_start: 0.7286 (mp) cc_final: 0.7040 (mm) REVERT: A 707 ARG cc_start: 0.7315 (tpp80) cc_final: 0.6834 (mmm160) REVERT: A 713 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8086 (mmm) REVERT: A 774 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7786 (mt-10) outliers start: 43 outliers final: 23 residues processed: 181 average time/residue: 0.9730 time to fit residues: 193.5167 Evaluate side-chains 182 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 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 638 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL 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 463 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 587 LEU 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: 0.9990 chunk 117 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 B 720 ASN B 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119091 restraints weight = 17817.343| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.59 r_work: 0.3107 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10912 Z= 0.148 Angle : 0.515 7.206 14884 Z= 0.266 Chirality : 0.042 0.142 1710 Planarity : 0.003 0.038 1806 Dihedral : 7.102 59.524 1952 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.45 % Allowed : 20.14 % Favored : 76.41 % 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: 1.80 (0.23), residues: 1268 helix: 2.55 (0.20), residues: 584 sheet: 1.04 (0.29), residues: 284 loop : -0.79 (0.29), residues: 400 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 0.025 0.002 TYR A 605 ARG 0.004 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 634) hydrogen bonds : angle 4.54796 ( 1822) metal coordination : bond 0.00675 ( 6) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.77467 ( 16) covalent geometry : bond 0.00350 (10898) covalent geometry : angle 0.51199 (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 190 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.140 Fit side-chains REVERT: B 118 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6483 (mtp180) REVERT: B 152 MET cc_start: 0.8525 (mtt) cc_final: 0.8220 (mtt) REVERT: B 158 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: B 207 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: B 297 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8418 (mm) REVERT: B 576 SER cc_start: 0.8490 (m) cc_final: 0.8093 (p) REVERT: B 684 MET cc_start: 0.5708 (tmt) cc_final: 0.5243 (mpm) REVERT: B 702 LEU cc_start: 0.7638 (tp) cc_final: 0.7315 (tt) REVERT: B 707 ARG cc_start: 0.7355 (tpp80) cc_final: 0.6833 (mmm160) REVERT: B 738 LYS cc_start: 0.7579 (mttt) cc_final: 0.6988 (mtmm) REVERT: B 753 MET cc_start: 0.8731 (mmt) cc_final: 0.8162 (mmt) REVERT: A 83 ASN cc_start: 0.8444 (p0) cc_final: 0.8140 (p0) REVERT: A 118 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6436 (mtp180) REVERT: A 158 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: A 207 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: A 297 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8415 (mm) REVERT: A 536 TYR cc_start: 0.7632 (m-80) cc_final: 0.7397 (m-80) REVERT: A 576 SER cc_start: 0.8613 (m) cc_final: 0.8200 (p) REVERT: A 684 MET cc_start: 0.5700 (tmt) cc_final: 0.5160 (mpm) REVERT: A 692 LEU cc_start: 0.7245 (mp) cc_final: 0.7016 (mm) REVERT: A 707 ARG cc_start: 0.7386 (tpp80) cc_final: 0.6849 (mmm160) REVERT: A 713 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: A 753 MET cc_start: 0.8698 (mmt) cc_final: 0.8059 (mmt) REVERT: A 774 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7883 (mt-10) outliers start: 39 outliers final: 23 residues processed: 174 average time/residue: 0.9688 time to fit residues: 185.5311 Evaluate side-chains 181 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 221 MET 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 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 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 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 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: 0.8980 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.151174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117661 restraints weight = 14082.068| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.93 r_work: 0.3130 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10912 Z= 0.185 Angle : 0.553 7.661 14884 Z= 0.282 Chirality : 0.043 0.143 1710 Planarity : 0.003 0.038 1806 Dihedral : 7.143 59.357 1952 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.89 % Allowed : 19.70 % Favored : 76.41 % 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: 1.75 (0.23), residues: 1268 helix: 2.48 (0.20), residues: 584 sheet: 1.17 (0.30), residues: 272 loop : -0.85 (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 0.029 0.002 TYR A 605 ARG 0.004 0.001 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 634) hydrogen bonds : angle 4.57532 ( 1822) metal coordination : bond 0.00727 ( 6) SS BOND : bond 0.00282 ( 8) SS BOND : angle 1.98120 ( 16) covalent geometry : bond 0.00446 (10898) covalent geometry : angle 0.54897 (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 195 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.072 Fit side-chains REVERT: B 118 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6545 (mtp180) REVERT: B 152 MET cc_start: 0.8552 (mtt) cc_final: 0.8253 (mtt) REVERT: B 158 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: B 207 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 274 SER cc_start: 0.7222 (OUTLIER) cc_final: 0.7010 (t) REVERT: B 297 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8503 (mm) REVERT: B 576 SER cc_start: 0.8484 (m) cc_final: 0.8077 (p) REVERT: B 684 MET cc_start: 0.5811 (tmt) cc_final: 0.5331 (mpm) REVERT: B 707 ARG cc_start: 0.7368 (tpp80) cc_final: 0.6861 (mmm160) REVERT: B 738 LYS cc_start: 0.7566 (mttt) cc_final: 0.7049 (mtmm) REVERT: B 753 MET cc_start: 0.8679 (mmt) cc_final: 0.8069 (mmt) REVERT: A 118 ARG cc_start: 0.7246 (ttm-80) cc_final: 0.6437 (mtp180) REVERT: A 158 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: A 207 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: A 297 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8495 (mm) REVERT: A 536 TYR cc_start: 0.7665 (m-80) cc_final: 0.7401 (m-80) REVERT: A 576 SER cc_start: 0.8547 (m) cc_final: 0.8114 (p) REVERT: A 684 MET cc_start: 0.5672 (tmt) cc_final: 0.5159 (mpm) REVERT: A 692 LEU cc_start: 0.7286 (mp) cc_final: 0.7003 (mm) REVERT: A 707 ARG cc_start: 0.7361 (tpp80) cc_final: 0.6844 (mmm160) REVERT: A 713 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: A 774 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7848 (mt-10) outliers start: 44 outliers final: 27 residues processed: 177 average time/residue: 0.9115 time to fit residues: 178.2680 Evaluate side-chains 185 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.152448 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 = 22982.077| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.72 r_work: 0.3007 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10912 Z= 0.161 Angle : 0.527 7.212 14884 Z= 0.271 Chirality : 0.042 0.141 1710 Planarity : 0.003 0.038 1806 Dihedral : 7.064 58.605 1952 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.53 % Allowed : 19.96 % Favored : 76.50 % 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: 1.81 (0.23), residues: 1268 helix: 2.54 (0.20), residues: 584 sheet: 1.16 (0.30), residues: 272 loop : -0.81 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.005 0.001 HIS B 563 PHE 0.011 0.001 PHE B 317 TYR 0.031 0.002 TYR A 605 ARG 0.004 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 634) hydrogen bonds : angle 4.52488 ( 1822) metal coordination : bond 0.00694 ( 6) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.87092 ( 16) covalent geometry : bond 0.00384 (10898) covalent geometry : angle 0.52371 (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 189 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.199 Fit side-chains REVERT: B 118 ARG cc_start: 0.7244 (ttm-80) cc_final: 0.6466 (mtp180) REVERT: B 152 MET cc_start: 0.8475 (mtt) cc_final: 0.8184 (mtt) REVERT: B 158 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: B 207 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 297 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8438 (mm) REVERT: B 576 SER cc_start: 0.8441 (m) cc_final: 0.8013 (p) REVERT: B 577 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: B 684 MET cc_start: 0.5770 (tmt) cc_final: 0.5300 (mpm) REVERT: B 702 LEU cc_start: 0.7604 (tp) cc_final: 0.7249 (tt) REVERT: B 707 ARG cc_start: 0.7299 (tpp80) cc_final: 0.6787 (mmm160) REVERT: B 738 LYS cc_start: 0.7487 (mttt) cc_final: 0.6958 (mtmm) REVERT: B 753 MET cc_start: 0.8658 (mmt) cc_final: 0.8073 (mmt) REVERT: A 118 ARG cc_start: 0.7220 (ttm-80) cc_final: 0.6420 (mtp180) REVERT: A 158 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: A 207 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: A 297 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 524 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6354 (mtt180) REVERT: A 536 TYR cc_start: 0.7609 (m-80) cc_final: 0.7334 (m-80) REVERT: A 576 SER cc_start: 0.8501 (m) cc_final: 0.8052 (p) REVERT: A 684 MET cc_start: 0.5818 (tmt) cc_final: 0.5314 (mpm) REVERT: A 692 LEU cc_start: 0.7014 (mp) cc_final: 0.6810 (mm) REVERT: A 707 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6782 (mmm160) REVERT: A 713 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8016 (mmm) REVERT: A 753 MET cc_start: 0.8627 (mmt) cc_final: 0.7982 (mmt) REVERT: A 774 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7781 (mt-10) outliers start: 40 outliers final: 26 residues processed: 176 average time/residue: 0.9942 time to fit residues: 193.3221 Evaluate side-chains 183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 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 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 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 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: 2.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 A 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.149973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116052 restraints weight = 14877.055| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.96 r_work: 0.3102 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10912 Z= 0.221 Angle : 0.589 8.342 14884 Z= 0.300 Chirality : 0.044 0.142 1710 Planarity : 0.004 0.039 1806 Dihedral : 7.258 58.577 1952 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.98 % Allowed : 19.61 % Favored : 76.41 % 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: 1.63 (0.23), residues: 1268 helix: 2.38 (0.20), residues: 584 sheet: 1.11 (0.30), residues: 272 loop : -0.90 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 629 HIS 0.005 0.001 HIS B 563 PHE 0.013 0.002 PHE A 632 TYR 0.043 0.002 TYR A 605 ARG 0.005 0.001 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 634) hydrogen bonds : angle 4.64961 ( 1822) metal coordination : bond 0.00820 ( 6) SS BOND : bond 0.00349 ( 8) SS BOND : angle 2.21036 ( 16) covalent geometry : bond 0.00537 (10898) covalent geometry : angle 0.58466 (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 191 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 1.064 Fit side-chains REVERT: B 118 ARG cc_start: 0.7332 (ttm-80) cc_final: 0.6530 (mtp180) REVERT: B 152 MET cc_start: 0.8507 (mtt) cc_final: 0.8188 (mtt) REVERT: B 158 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: B 207 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: B 297 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8548 (mm) REVERT: B 519 ASP cc_start: 0.7064 (t0) cc_final: 0.6792 (t70) REVERT: B 576 SER cc_start: 0.8526 (m) cc_final: 0.8059 (p) REVERT: B 577 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: B 684 MET cc_start: 0.5846 (tmt) cc_final: 0.5357 (mpm) REVERT: B 702 LEU cc_start: 0.7599 (tp) cc_final: 0.7268 (tt) REVERT: B 707 ARG cc_start: 0.7390 (tpp80) cc_final: 0.6858 (mmm160) REVERT: B 738 LYS cc_start: 0.7601 (mttt) cc_final: 0.7079 (mtmm) REVERT: A 118 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6470 (mtp180) REVERT: A 158 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: A 207 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: A 297 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 524 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6426 (mtt180) REVERT: A 536 TYR cc_start: 0.7678 (m-80) cc_final: 0.7410 (m-80) REVERT: A 576 SER cc_start: 0.8430 (m) cc_final: 0.7978 (p) REVERT: A 684 MET cc_start: 0.5885 (tmt) cc_final: 0.5347 (mpm) REVERT: A 707 ARG cc_start: 0.7403 (tpp80) cc_final: 0.6854 (mmm160) REVERT: A 713 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8118 (mmm) REVERT: A 774 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7891 (mt-10) outliers start: 45 outliers final: 29 residues processed: 173 average time/residue: 1.0608 time to fit residues: 201.8238 Evaluate side-chains 182 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 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 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 713 MET Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 764 ASN 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: 0.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 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 A 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119378 restraints weight = 22157.308| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.25 r_work: 0.3073 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 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 = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10912 Z= 0.153 Angle : 0.532 7.260 14884 Z= 0.273 Chirality : 0.042 0.141 1710 Planarity : 0.003 0.038 1806 Dihedral : 7.121 58.037 1952 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.45 % Allowed : 19.96 % 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: 1.76 (0.23), residues: 1268 helix: 2.49 (0.20), residues: 584 sheet: 1.11 (0.30), residues: 272 loop : -0.79 (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 A 697 TYR 0.032 0.002 TYR A 605 ARG 0.004 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 634) hydrogen bonds : angle 4.55513 ( 1822) metal coordination : bond 0.00728 ( 6) SS BOND : bond 0.00295 ( 8) SS BOND : angle 1.89005 ( 16) covalent geometry : bond 0.00363 (10898) covalent geometry : angle 0.52832 (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 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: B 118 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.6544 (mtp180) REVERT: B 158 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: B 207 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: B 297 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 576 SER cc_start: 0.8462 (m) cc_final: 0.8041 (p) REVERT: B 577 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: B 684 MET cc_start: 0.5769 (tmt) cc_final: 0.5291 (mpm) REVERT: B 702 LEU cc_start: 0.7626 (tp) cc_final: 0.7308 (tt) REVERT: B 707 ARG cc_start: 0.7346 (tpp80) cc_final: 0.6858 (mmm160) REVERT: B 720 ASN cc_start: 0.8083 (m110) cc_final: 0.7786 (m110) REVERT: B 738 LYS cc_start: 0.7526 (mttt) cc_final: 0.7008 (mtmm) REVERT: B 753 MET cc_start: 0.8663 (mmt) cc_final: 0.8069 (mmt) REVERT: A 118 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.6411 (mtp180) REVERT: A 158 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: A 207 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: A 297 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8399 (mm) REVERT: A 536 TYR cc_start: 0.7656 (m-80) cc_final: 0.7391 (m-80) REVERT: A 576 SER cc_start: 0.8380 (m) cc_final: 0.7941 (p) REVERT: A 684 MET cc_start: 0.5814 (tmt) cc_final: 0.5341 (mpm) REVERT: A 702 LEU cc_start: 0.7737 (tp) cc_final: 0.7374 (tt) REVERT: A 707 ARG cc_start: 0.7365 (tpp80) cc_final: 0.6859 (mmm160) REVERT: A 713 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8076 (mmm) REVERT: A 753 MET cc_start: 0.8665 (mmt) cc_final: 0.8030 (mmt) REVERT: A 774 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7788 (mt-10) outliers start: 39 outliers final: 28 residues processed: 172 average time/residue: 1.4761 time to fit residues: 280.6871 Evaluate side-chains 181 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 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 692 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 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 444 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 81 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6006 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.153090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120317 restraints weight = 18849.808| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.93 r_work: 0.3091 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10912 Z= 0.130 Angle : 0.497 6.236 14884 Z= 0.257 Chirality : 0.041 0.139 1710 Planarity : 0.003 0.038 1806 Dihedral : 6.952 57.591 1952 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.74 % Allowed : 20.58 % Favored : 76.68 % 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: 1.93 (0.23), residues: 1268 helix: 2.63 (0.20), residues: 584 sheet: 1.18 (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 487 PHE 0.011 0.001 PHE B 317 TYR 0.024 0.001 TYR A 605 ARG 0.003 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 634) hydrogen bonds : angle 4.46499 ( 1822) metal coordination : bond 0.00653 ( 6) SS BOND : bond 0.00266 ( 8) SS BOND : angle 1.58630 ( 16) covalent geometry : bond 0.00306 (10898) covalent geometry : angle 0.49495 (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 183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.214 Fit side-chains REVERT: B 118 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.6562 (mtp180) REVERT: B 158 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 207 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: B 297 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8417 (mm) REVERT: B 576 SER cc_start: 0.8473 (m) cc_final: 0.8034 (p) REVERT: B 577 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: B 684 MET cc_start: 0.6081 (tmt) cc_final: 0.5510 (mpm) REVERT: B 702 LEU cc_start: 0.7606 (tp) cc_final: 0.7264 (tt) REVERT: B 707 ARG cc_start: 0.7365 (tpp80) cc_final: 0.6796 (mmm160) REVERT: B 713 MET cc_start: 0.8174 (mmm) cc_final: 0.7915 (mtp) REVERT: B 720 ASN cc_start: 0.8031 (m110) cc_final: 0.7710 (m110) REVERT: B 738 LYS cc_start: 0.7463 (mttt) cc_final: 0.6994 (mtmm) REVERT: B 753 MET cc_start: 0.8677 (mmt) cc_final: 0.8210 (mmt) REVERT: A 83 ASN cc_start: 0.8414 (p0) cc_final: 0.8108 (p0) REVERT: A 118 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6379 (mtp180) REVERT: A 158 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: A 207 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: A 297 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 519 ASP cc_start: 0.7060 (t0) cc_final: 0.6694 (t70) REVERT: A 536 TYR cc_start: 0.7686 (m-80) cc_final: 0.7430 (m-80) REVERT: A 576 SER cc_start: 0.8610 (m) cc_final: 0.8134 (p) REVERT: A 684 MET cc_start: 0.5941 (tmt) cc_final: 0.5389 (mpm) REVERT: A 702 LEU cc_start: 0.7711 (tp) cc_final: 0.7355 (tt) REVERT: A 707 ARG cc_start: 0.7401 (tpp80) cc_final: 0.6823 (mmm160) REVERT: A 713 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8129 (mmm) REVERT: A 738 LYS cc_start: 0.7231 (mtpm) cc_final: 0.6001 (mmtp) REVERT: A 753 MET cc_start: 0.8678 (mmt) cc_final: 0.8165 (mmt) REVERT: A 774 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7840 (mt-10) outliers start: 31 outliers final: 23 residues processed: 170 average time/residue: 0.9613 time to fit residues: 179.7379 Evaluate side-chains 179 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 692 LEU Chi-restraints excluded: chain B residue 782 CYS 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 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 463 VAL 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 66 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.152484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120534 restraints weight = 27711.043| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.18 r_work: 0.3008 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10912 Z= 0.152 Angle : 0.516 6.458 14884 Z= 0.265 Chirality : 0.042 0.140 1710 Planarity : 0.003 0.037 1806 Dihedral : 6.947 57.807 1951 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.92 % Allowed : 20.58 % Favored : 76.50 % 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: 1.91 (0.23), residues: 1268 helix: 2.61 (0.20), residues: 584 sheet: 1.19 (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 563 PHE 0.016 0.001 PHE A 697 TYR 0.029 0.002 TYR A 605 ARG 0.003 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 634) hydrogen bonds : angle 4.47164 ( 1822) metal coordination : bond 0.00691 ( 6) SS BOND : bond 0.00231 ( 8) SS BOND : angle 1.69772 ( 16) covalent geometry : bond 0.00364 (10898) covalent geometry : angle 0.51304 (14868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8684.25 seconds wall clock time: 153 minutes 1.24 seconds (9181.24 seconds total)