Starting phenix.real_space_refine on Thu Jul 2 22:19:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6m_36008/07_2026/8j6m_36008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6m_36008/07_2026/8j6m_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_2026/8j6m_36008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6m_36008/07_2026/8j6m_36008.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6m_36008/07_2026/8j6m_36008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6m_36008/07_2026/8j6m_36008.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.153 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'ASP:plan': 1, 'TRP: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, 'ASP:plan': 1, 'TRP: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, 'ASP:plan': 1, 'TRP: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, 'ASP:plan': 1, 'TRP: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, 133 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {' ZN': 1, 'CLR': 4, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 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: 4.09, per 1000 atoms: 0.39 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: 0.87 Conformation dependent library (CDL) restraints added in 887.1 milliseconds 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: 0.25 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: 1.48 Time building geometry restraints manager: 1.17 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.960 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG A 289 TYR 0.021 0.002 TYR B 605 PHE 0.023 0.002 PHE A 317 TRP 0.016 0.002 TRP A 106 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.55 (10898) covalent geometry : angle 1.10424 / 0.70 (14868) SS BOND : bond 0.01515 / 0.97 ( 8) SS BOND : angle 3.71678 / 2.36 ( 16) hydrogen bonds : bond 0.19433 / 12.94 ( 634) hydrogen bonds : angle 7.38516 / 5.18 ( 1822) metal coordination : bond 0.16225 / 8.83 ( 6) *********************** 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 : 0.376 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: 0.5847 (tmt) cc_final: 0.5296 (mpp) REVERT: B 702 LEU cc_start: 0.7717 (tp) cc_final: 0.7303 (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: 0.5114 (mpp) REVERT: A 707 ARG cc_start: 0.7280 (tpp80) cc_final: 0.6967 (mmm160) REVERT: A 774 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7658 (mt-10) outliers start: 18 outliers final: 9 residues processed: 203 average time/residue: 0.4823 time to fit residues: 107.0635 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 : 0.379 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 461 GLN B 720 ASN A 461 GLN A 475 ASN A 541 HIS A 636 HIS A 646 GLN A 694 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120549 restraints weight = 13441.459| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.89 r_work: 0.3168 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10912 Z= 0.166 Angle : 0.609 7.790 14884 Z= 0.311 Chirality : 0.044 0.154 1710 Planarity : 0.004 0.036 1806 Dihedral : 8.787 60.411 1964 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.92 % Allowed : 18.29 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.22), residues: 1268 helix: 2.24 (0.19), residues: 584 sheet: 1.31 (0.28), residues: 284 loop : -0.81 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 172 TYR 0.014 0.002 TYR B 605 PHE 0.021 0.002 PHE A 317 TRP 0.012 0.001 TRP B 629 HIS 0.004 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (10898) covalent geometry : angle 0.60529 / 0.31 (14868) SS BOND : bond 0.00243 / 0.14 ( 8) SS BOND : angle 2.12650 / 1.58 ( 16) hydrogen bonds : bond 0.05305 / 3.55 ( 634) hydrogen bonds : angle 5.00215 / 3.52 ( 1822) metal coordination : bond 0.01300 / 0.62 ( 6) *********************** 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: 33 poor density : 172 time to evaluate : 0.401 Fit side-chains REVERT: B 90 ASN cc_start: 0.7857 (m-40) cc_final: 0.7652 (m-40) REVERT: B 118 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.6646 (mtp180) REVERT: B 158 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: B 536 TYR cc_start: 0.7316 (m-80) cc_final: 0.7108 (m-80) REVERT: B 576 SER cc_start: 0.8321 (m) cc_final: 0.8004 (p) REVERT: B 684 MET cc_start: 0.5767 (tmt) cc_final: 0.4953 (mpp) REVERT: B 702 LEU cc_start: 0.7617 (tp) cc_final: 0.7249 (tt) REVERT: B 707 ARG cc_start: 0.7223 (tpp80) cc_final: 0.6785 (mmm160) REVERT: B 738 LYS cc_start: 0.7636 (mttt) cc_final: 0.7190 (mtpm) REVERT: A 83 ASN cc_start: 0.8086 (p0) cc_final: 0.7676 (p0) REVERT: A 118 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.6501 (mtp180) REVERT: A 158 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: A 302 LYS cc_start: 0.7925 (mptm) cc_final: 0.7633 (mmtm) REVERT: A 536 TYR cc_start: 0.7275 (m-80) cc_final: 0.6997 (m-80) REVERT: A 576 SER cc_start: 0.8298 (m) cc_final: 0.8008 (p) REVERT: A 684 MET cc_start: 0.5521 (tmt) cc_final: 0.4843 (mpp) REVERT: A 692 LEU cc_start: 0.7312 (mp) cc_final: 0.7056 (mp) REVERT: A 697 PHE cc_start: 0.7599 (t80) cc_final: 0.7387 (t80) REVERT: A 707 ARG cc_start: 0.7207 (tpp80) cc_final: 0.6732 (mmm160) REVERT: A 720 ASN cc_start: 0.8312 (m-40) cc_final: 0.7987 (m110) REVERT: A 738 LYS cc_start: 0.6934 (mtpm) cc_final: 0.5716 (mmtp) REVERT: A 774 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7842 (mt-10) outliers start: 33 outliers final: 18 residues processed: 193 average time/residue: 0.4244 time to fit residues: 90.5180 Evaluate side-chains 177 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 713 MET 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 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 596 ASP 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 106 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 GLN B 720 ASN B 779 ASN A 646 GLN A 764 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.153263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119674 restraints weight = 15036.335| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.98 r_work: 0.3150 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10912 Z= 0.154 Angle : 0.539 6.787 14884 Z= 0.278 Chirality : 0.043 0.143 1710 Planarity : 0.003 0.037 1806 Dihedral : 7.287 56.786 1956 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.53 % Allowed : 18.64 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.22), residues: 1268 helix: 2.56 (0.19), residues: 584 sheet: 1.21 (0.29), residues: 284 loop : -0.75 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 172 TYR 0.017 0.002 TYR A 605 PHE 0.015 0.001 PHE A 317 TRP 0.011 0.001 TRP A 106 HIS 0.004 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (10898) covalent geometry : angle 0.53547 / 0.28 (14868) SS BOND : bond 0.00185 / 0.10 ( 8) SS BOND : angle 1.84759 / 1.35 ( 16) hydrogen bonds : bond 0.04536 / 3.04 ( 634) hydrogen bonds : angle 4.61202 / 3.26 ( 1822) metal coordination : bond 0.00692 / 0.35 ( 6) *********************** 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 205 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.389 Fit side-chains REVERT: B 118 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6538 (mtp180) REVERT: B 297 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 576 SER cc_start: 0.8472 (m) cc_final: 0.8063 (p) REVERT: B 684 MET cc_start: 0.5561 (tmt) cc_final: 0.5160 (mpp) REVERT: B 702 LEU cc_start: 0.7609 (tp) cc_final: 0.7255 (tt) REVERT: B 707 ARG cc_start: 0.7238 (tpp80) cc_final: 0.6857 (mmm160) REVERT: B 738 LYS cc_start: 0.7742 (mttt) cc_final: 0.7234 (mtmm) REVERT: A 90 ASN cc_start: 0.7903 (m-40) cc_final: 0.7603 (m-40) REVERT: A 118 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6394 (mtp180) REVERT: A 297 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 302 LYS cc_start: 0.7844 (mptm) cc_final: 0.7547 (mmmm) REVERT: A 536 TYR cc_start: 0.7457 (m-80) cc_final: 0.7146 (m-80) REVERT: A 576 SER cc_start: 0.8409 (m) cc_final: 0.8027 (p) REVERT: A 684 MET cc_start: 0.5427 (tmt) cc_final: 0.5018 (mpm) REVERT: A 692 LEU cc_start: 0.7338 (mp) cc_final: 0.7086 (mp) REVERT: A 697 PHE cc_start: 0.7556 (t80) cc_final: 0.7351 (t80) REVERT: A 707 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6851 (mmm160) REVERT: A 738 LYS cc_start: 0.6997 (mtpm) cc_final: 0.6159 (mtmm) REVERT: A 774 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7884 (mt-10) outliers start: 40 outliers final: 21 residues processed: 188 average time/residue: 0.3983 time to fit residues: 82.9928 Evaluate side-chains 179 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL 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 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU 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 587 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 HIS A 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.152822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119247 restraints weight = 14418.484| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.96 r_work: 0.3146 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1950 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= 0.158 Angle : 0.528 6.477 14884 Z= 0.272 Chirality : 0.042 0.144 1710 Planarity : 0.003 0.037 1806 Dihedral : 7.124 58.652 1953 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.71 % Allowed : 18.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1268 helix: 2.59 (0.20), residues: 584 sheet: 1.16 (0.29), residues: 284 loop : -0.75 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 172 TYR 0.023 0.002 TYR A 605 PHE 0.013 0.001 PHE A 317 TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (10898) covalent geometry : angle 0.52516 / 0.27 (14868) SS BOND : bond 0.00205 / 0.12 ( 8) SS BOND : angle 1.84473 / 1.36 ( 16) hydrogen bonds : bond 0.04350 / 2.93 ( 634) hydrogen bonds : angle 4.57121 / 3.24 ( 1822) metal coordination : bond 0.00699 / 0.35 ( 6) *********************** 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 200 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.402 Fit side-chains REVERT: B 118 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6505 (mtp180) REVERT: B 158 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: B 207 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: B 274 SER cc_start: 0.7246 (OUTLIER) cc_final: 0.7036 (t) REVERT: B 297 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8513 (mm) REVERT: B 576 SER cc_start: 0.8432 (m) cc_final: 0.8047 (p) REVERT: B 684 MET cc_start: 0.5565 (tmt) cc_final: 0.5103 (mpm) REVERT: B 702 LEU cc_start: 0.7612 (tp) cc_final: 0.7283 (tt) REVERT: B 707 ARG cc_start: 0.7302 (tpp80) cc_final: 0.6845 (mmm160) REVERT: B 738 LYS cc_start: 0.7560 (mttt) cc_final: 0.7008 (mtmm) REVERT: B 753 MET cc_start: 0.8650 (mmt) cc_final: 0.8047 (mmt) REVERT: A 90 ASN cc_start: 0.7927 (m-40) cc_final: 0.7642 (m-40) REVERT: A 118 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6371 (mtp180) REVERT: A 158 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: A 207 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: A 297 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8374 (mm) REVERT: A 536 TYR cc_start: 0.7540 (m-80) cc_final: 0.7280 (m-80) REVERT: A 576 SER cc_start: 0.8586 (m) cc_final: 0.8176 (p) REVERT: A 684 MET cc_start: 0.5457 (tmt) cc_final: 0.5017 (mpm) REVERT: A 692 LEU cc_start: 0.7271 (mp) cc_final: 0.7017 (mm) REVERT: A 707 ARG cc_start: 0.7318 (tpp80) cc_final: 0.6854 (mmm160) REVERT: A 713 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8101 (mmm) REVERT: A 738 LYS cc_start: 0.7073 (mtpm) cc_final: 0.6227 (mtmm) REVERT: A 774 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7818 (mt-10) outliers start: 42 outliers final: 25 residues processed: 182 average time/residue: 0.4180 time to fit residues: 84.2642 Evaluate side-chains 188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.149137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115789 restraints weight = 17902.284| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.53 r_work: 0.3065 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 10912 Z= 0.260 Angle : 0.633 8.896 14884 Z= 0.323 Chirality : 0.046 0.154 1710 Planarity : 0.004 0.039 1806 Dihedral : 7.416 59.796 1951 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.24 % Allowed : 18.99 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.22), residues: 1268 helix: 2.23 (0.20), residues: 584 sheet: 1.14 (0.30), residues: 272 loop : -0.99 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 593 TYR 0.028 0.002 TYR A 605 PHE 0.014 0.002 PHE B 632 TRP 0.012 0.002 TRP B 629 HIS 0.006 0.002 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.26 (10898) covalent geometry : angle 0.62814 / 0.32 (14868) SS BOND : bond 0.00404 / 0.24 ( 8) SS BOND : angle 2.46962 / 1.80 ( 16) hydrogen bonds : bond 0.05028 / 3.38 ( 634) hydrogen bonds : angle 4.77457 / 3.37 ( 1822) metal coordination : bond 0.00886 / 0.44 ( 6) *********************** 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 195 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.464 Fit side-chains REVERT: B 118 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.6547 (mtp180) REVERT: B 158 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: B 207 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 274 SER cc_start: 0.7233 (OUTLIER) cc_final: 0.6976 (t) REVERT: B 576 SER cc_start: 0.8545 (m) cc_final: 0.8119 (p) REVERT: B 684 MET cc_start: 0.5724 (tmt) cc_final: 0.5202 (mpm) REVERT: B 702 LEU cc_start: 0.7659 (tp) cc_final: 0.7339 (tt) REVERT: B 707 ARG cc_start: 0.7408 (tpp80) cc_final: 0.6870 (mmm160) REVERT: B 738 LYS cc_start: 0.7781 (mttt) cc_final: 0.7328 (mtmm) REVERT: A 83 ASN cc_start: 0.8684 (p0) cc_final: 0.8386 (p0) REVERT: A 90 ASN cc_start: 0.7942 (m-40) cc_final: 0.7691 (m-40) REVERT: A 118 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.6414 (mtp180) REVERT: A 158 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: A 207 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: A 524 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6500 (mtt180) REVERT: A 536 TYR cc_start: 0.7596 (m-80) cc_final: 0.7370 (m-80) REVERT: A 576 SER cc_start: 0.8475 (m) cc_final: 0.8049 (p) REVERT: A 684 MET cc_start: 0.5579 (tmt) cc_final: 0.5047 (mpm) REVERT: A 692 LEU cc_start: 0.7233 (mp) cc_final: 0.6929 (mm) REVERT: A 702 LEU cc_start: 0.7628 (tp) cc_final: 0.7246 (tt) REVERT: A 707 ARG cc_start: 0.7422 (tpp80) cc_final: 0.6769 (mmm160) REVERT: A 713 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8140 (mmm) REVERT: A 774 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7810 (mt-10) outliers start: 48 outliers final: 27 residues processed: 174 average time/residue: 0.4315 time to fit residues: 82.6338 Evaluate side-chains 178 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 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 713 MET 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 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 7 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120340 restraints weight = 22157.846| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.28 r_work: 0.3083 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10912 Z= 0.134 Angle : 0.507 7.094 14884 Z= 0.261 Chirality : 0.042 0.144 1710 Planarity : 0.003 0.039 1806 Dihedral : 7.067 58.712 1951 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.62 % Allowed : 19.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.23), residues: 1268 helix: 2.59 (0.20), residues: 584 sheet: 1.00 (0.30), residues: 284 loop : -0.75 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 172 TYR 0.028 0.002 TYR A 605 PHE 0.012 0.001 PHE B 317 TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10898) covalent geometry : angle 0.50405 / 0.26 (14868) SS BOND : bond 0.00263 / 0.16 ( 8) SS BOND : angle 1.76797 / 1.32 ( 16) hydrogen bonds : bond 0.04102 / 2.75 ( 634) hydrogen bonds : angle 4.53437 / 3.21 ( 1822) metal coordination : bond 0.00649 / 0.33 ( 6) *********************** 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: 41 poor density : 154 time to evaluate : 0.400 Fit side-chains REVERT: B 118 ARG cc_start: 0.7217 (ttm-80) cc_final: 0.6524 (mtp180) REVERT: B 158 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: B 207 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: B 576 SER cc_start: 0.8452 (m) cc_final: 0.8079 (p) REVERT: B 684 MET cc_start: 0.5747 (tmt) cc_final: 0.5315 (mpm) REVERT: B 707 ARG cc_start: 0.7307 (tpp80) cc_final: 0.6831 (mmm160) REVERT: B 738 LYS cc_start: 0.7517 (mttt) cc_final: 0.7003 (mtmm) REVERT: B 753 MET cc_start: 0.8688 (mmt) cc_final: 0.8136 (mmt) REVERT: A 90 ASN cc_start: 0.7878 (m-40) cc_final: 0.7656 (m-40) REVERT: A 118 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6454 (mtp180) REVERT: A 158 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: A 207 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 536 TYR cc_start: 0.7612 (m-80) cc_final: 0.7350 (m-80) REVERT: A 576 SER cc_start: 0.8583 (m) cc_final: 0.8162 (p) REVERT: A 684 MET cc_start: 0.5571 (tmt) cc_final: 0.5132 (mpm) REVERT: A 692 LEU cc_start: 0.7130 (mp) cc_final: 0.6913 (mm) REVERT: A 707 ARG cc_start: 0.7362 (tpp80) cc_final: 0.6869 (mmm160) REVERT: A 713 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8054 (mmm) REVERT: A 753 MET cc_start: 0.8652 (mmt) cc_final: 0.8006 (mmt) REVERT: A 774 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7756 (mt-10) outliers start: 41 outliers final: 25 residues processed: 179 average time/residue: 0.4078 time to fit residues: 80.4578 Evaluate side-chains 180 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 463 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 713 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.118202 restraints weight = 24047.238| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.83 r_work: 0.2968 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10912 Z= 0.200 Angle : 0.570 7.937 14884 Z= 0.290 Chirality : 0.044 0.143 1710 Planarity : 0.004 0.039 1806 Dihedral : 7.176 59.057 1951 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.15 % Allowed : 19.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.23), residues: 1268 helix: 2.47 (0.20), residues: 584 sheet: 1.11 (0.30), residues: 272 loop : -0.88 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 593 TYR 0.032 0.002 TYR A 605 PHE 0.012 0.002 PHE B 632 TRP 0.010 0.002 TRP B 629 HIS 0.005 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (10898) covalent geometry : angle 0.56586 / 0.29 (14868) SS BOND : bond 0.00311 / 0.18 ( 8) SS BOND : angle 2.09648 / 1.53 ( 16) hydrogen bonds : bond 0.04527 / 3.03 ( 634) hydrogen bonds : angle 4.59908 / 3.25 ( 1822) metal coordination : bond 0.00785 / 0.40 ( 6) *********************** 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 194 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.426 Fit side-chains REVERT: B 118 ARG cc_start: 0.7345 (ttm-80) cc_final: 0.6615 (mtp180) REVERT: B 158 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: B 207 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: B 297 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8433 (mm) REVERT: B 576 SER cc_start: 0.8496 (m) cc_final: 0.8084 (p) REVERT: B 577 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: B 684 MET cc_start: 0.5823 (tmt) cc_final: 0.5344 (mpm) REVERT: B 702 LEU cc_start: 0.7609 (tp) cc_final: 0.7251 (tt) REVERT: B 707 ARG cc_start: 0.7407 (tpp80) cc_final: 0.6896 (mmm160) REVERT: B 738 LYS cc_start: 0.7634 (mttt) cc_final: 0.7125 (mtmm) REVERT: A 90 ASN cc_start: 0.8001 (m-40) cc_final: 0.7727 (m-40) REVERT: A 118 ARG cc_start: 0.7271 (ttm-80) cc_final: 0.6437 (mtp180) REVERT: A 158 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: A 207 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 297 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 454 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.6757 (t80) REVERT: A 524 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6473 (mtt180) REVERT: A 536 TYR cc_start: 0.7681 (m-80) cc_final: 0.7424 (m-80) REVERT: A 576 SER cc_start: 0.8433 (m) cc_final: 0.7999 (p) REVERT: A 684 MET cc_start: 0.5691 (tmt) cc_final: 0.5154 (mpm) REVERT: A 692 LEU cc_start: 0.7211 (mp) cc_final: 0.6993 (mm) REVERT: A 702 LEU cc_start: 0.7609 (tp) cc_final: 0.7246 (tt) REVERT: A 707 ARG cc_start: 0.7398 (tpp80) cc_final: 0.6886 (mmm160) REVERT: A 713 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8209 (mmm) REVERT: A 774 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7809 (mt-10) outliers start: 47 outliers final: 30 residues processed: 174 average time/residue: 0.4192 time to fit residues: 80.4021 Evaluate side-chains 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 713 MET 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 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 LEU 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 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3677 r_free = 0.3677 target = 0.150627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117694 restraints weight = 12454.808| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.81 r_work: 0.3144 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10912 Z= 0.190 Angle : 0.558 8.053 14884 Z= 0.285 Chirality : 0.043 0.141 1710 Planarity : 0.004 0.039 1806 Dihedral : 7.186 59.326 1951 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.80 % Allowed : 20.05 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.23), residues: 1268 helix: 2.45 (0.20), residues: 584 sheet: 1.10 (0.30), residues: 272 loop : -0.89 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 172 TYR 0.031 0.002 TYR A 605 PHE 0.012 0.002 PHE B 632 TRP 0.010 0.002 TRP B 629 HIS 0.005 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (10898) covalent geometry : angle 0.55415 / 0.28 (14868) SS BOND : bond 0.00318 / 0.19 ( 8) SS BOND : angle 2.09699 / 1.53 ( 16) hydrogen bonds : bond 0.04439 / 2.97 ( 634) hydrogen bonds : angle 4.60391 / 3.26 ( 1822) metal coordination : bond 0.00770 / 0.39 ( 6) *********************** 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 184 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.396 Fit side-chains REVERT: B 118 ARG cc_start: 0.7280 (ttm-80) cc_final: 0.6527 (mtp180) REVERT: B 158 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: B 207 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: B 297 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 576 SER cc_start: 0.8511 (m) cc_final: 0.8059 (p) REVERT: B 577 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: B 684 MET cc_start: 0.5775 (tmt) cc_final: 0.5344 (mpm) REVERT: B 702 LEU cc_start: 0.7579 (tp) cc_final: 0.7254 (tt) REVERT: B 707 ARG cc_start: 0.7355 (tpp80) cc_final: 0.6835 (mmm160) REVERT: B 738 LYS cc_start: 0.7565 (mttt) cc_final: 0.7036 (mtmm) REVERT: A 90 ASN cc_start: 0.7960 (m-40) cc_final: 0.7691 (m-40) REVERT: A 118 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6387 (mtp180) REVERT: A 158 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: A 207 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: A 297 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8357 (mm) REVERT: A 536 TYR cc_start: 0.7668 (m-80) cc_final: 0.7407 (m-80) REVERT: A 576 SER cc_start: 0.8392 (m) cc_final: 0.7943 (p) REVERT: A 684 MET cc_start: 0.5807 (tmt) cc_final: 0.5341 (mpm) REVERT: A 692 LEU cc_start: 0.7153 (mp) cc_final: 0.6939 (mm) REVERT: A 702 LEU cc_start: 0.7598 (tp) cc_final: 0.7242 (tt) REVERT: A 707 ARG cc_start: 0.7360 (tpp80) cc_final: 0.6839 (mmm160) REVERT: A 713 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8055 (mmm) REVERT: A 774 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7754 (mt-10) outliers start: 43 outliers final: 31 residues processed: 166 average time/residue: 0.4303 time to fit residues: 78.7971 Evaluate side-chains 180 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 764 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3692 r_free = 0.3692 target = 0.152064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119190 restraints weight = 19332.244| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.94 r_work: 0.3078 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10912 Z= 0.142 Angle : 0.523 7.447 14884 Z= 0.268 Chirality : 0.042 0.141 1710 Planarity : 0.003 0.038 1806 Dihedral : 7.071 58.712 1951 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.18 % Allowed : 20.58 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.23), residues: 1268 helix: 2.58 (0.20), residues: 584 sheet: 1.07 (0.30), residues: 272 loop : -0.79 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.031 0.002 TYR A 605 PHE 0.015 0.001 PHE A 697 TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (10898) covalent geometry : angle 0.51936 / 0.27 (14868) SS BOND : bond 0.00259 / 0.15 ( 8) SS BOND : angle 1.83289 / 1.34 ( 16) hydrogen bonds : bond 0.04149 / 2.77 ( 634) hydrogen bonds : angle 4.53290 / 3.21 ( 1822) metal coordination : bond 0.00714 / 0.36 ( 6) *********************** 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 180 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.305 Fit side-chains REVERT: B 118 ARG cc_start: 0.7357 (ttm-80) cc_final: 0.6556 (mtp180) REVERT: B 158 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: B 207 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: B 297 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8351 (mm) REVERT: B 576 SER cc_start: 0.8495 (m) cc_final: 0.8069 (p) REVERT: B 577 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: B 684 MET cc_start: 0.5881 (tmt) cc_final: 0.5295 (mpm) REVERT: B 702 LEU cc_start: 0.7631 (tp) cc_final: 0.7303 (tt) REVERT: B 707 ARG cc_start: 0.7368 (tpp80) cc_final: 0.6794 (mmm160) REVERT: B 738 LYS cc_start: 0.7560 (mttt) cc_final: 0.7031 (mtmm) REVERT: A 90 ASN cc_start: 0.8035 (m-40) cc_final: 0.7786 (m-40) REVERT: A 118 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6401 (mtp180) REVERT: A 158 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: A 207 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: A 297 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 519 ASP cc_start: 0.7089 (t0) cc_final: 0.6719 (t70) REVERT: A 536 TYR cc_start: 0.7691 (m-80) cc_final: 0.7438 (m-80) REVERT: A 576 SER cc_start: 0.8453 (m) cc_final: 0.8002 (p) REVERT: A 684 MET cc_start: 0.5931 (tmt) cc_final: 0.5335 (mpm) REVERT: A 692 LEU cc_start: 0.7133 (mp) cc_final: 0.6929 (mm) REVERT: A 702 LEU cc_start: 0.7559 (tp) cc_final: 0.7206 (tt) REVERT: A 707 ARG cc_start: 0.7422 (tpp80) cc_final: 0.6852 (mmm160) REVERT: A 713 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8113 (mmm) REVERT: A 753 MET cc_start: 0.8715 (mmt) cc_final: 0.8131 (mmt) outliers start: 36 outliers final: 25 residues processed: 166 average time/residue: 0.4114 time to fit residues: 75.0714 Evaluate side-chains 175 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 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 713 MET Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 713 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3708 r_free = 0.3708 target = 0.153512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119870 restraints weight = 17023.429| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.36 r_work: 0.3141 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10912 Z= 0.126 Angle : 0.489 6.161 14884 Z= 0.253 Chirality : 0.041 0.141 1710 Planarity : 0.003 0.038 1806 Dihedral : 6.878 58.105 1951 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.83 % Allowed : 20.85 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.23), residues: 1268 helix: 2.71 (0.20), residues: 584 sheet: 1.25 (0.31), residues: 268 loop : -0.74 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.027 0.001 TYR A 605 PHE 0.011 0.001 PHE B 317 TRP 0.007 0.001 TRP B 629 HIS 0.004 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10898) covalent geometry : angle 0.48655 / 0.25 (14868) SS BOND : bond 0.00197 / 0.11 ( 8) SS BOND : angle 1.53595 / 1.12 ( 16) hydrogen bonds : bond 0.03901 / 2.60 ( 634) hydrogen bonds : angle 4.44435 / 3.15 ( 1822) metal coordination : bond 0.00640 / 0.33 ( 6) ********************** 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 182 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.322 Fit side-chains REVERT: B 118 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.6513 (mtp180) REVERT: B 158 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: B 207 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 297 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8388 (mm) REVERT: B 576 SER cc_start: 0.8453 (m) cc_final: 0.8010 (p) REVERT: B 577 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 684 MET cc_start: 0.6055 (tmt) cc_final: 0.5531 (mpm) REVERT: B 696 SER cc_start: 0.7790 (m) cc_final: 0.7559 (p) REVERT: B 702 LEU cc_start: 0.7628 (tp) cc_final: 0.7284 (tt) REVERT: B 707 ARG cc_start: 0.7353 (tpp80) cc_final: 0.6819 (mmm160) REVERT: B 720 ASN cc_start: 0.8005 (m110) cc_final: 0.7703 (m110) REVERT: B 738 LYS cc_start: 0.7502 (mttt) cc_final: 0.7040 (mtmm) REVERT: B 753 MET cc_start: 0.8715 (mmt) cc_final: 0.8205 (mmt) REVERT: A 83 ASN cc_start: 0.8267 (p0) cc_final: 0.7933 (p0) REVERT: A 90 ASN cc_start: 0.7970 (m-40) cc_final: 0.7568 (m-40) REVERT: A 118 ARG cc_start: 0.7359 (ttm-80) cc_final: 0.6433 (mtp180) REVERT: A 158 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: A 207 GLU cc_start: 0.8051 (tp30) cc_final: 0.7249 (mp0) REVERT: A 294 GLU cc_start: 0.8688 (tt0) cc_final: 0.8470 (tm-30) REVERT: A 297 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 536 TYR cc_start: 0.7705 (m-80) cc_final: 0.7452 (m-80) REVERT: A 576 SER cc_start: 0.8584 (m) cc_final: 0.8110 (p) REVERT: A 684 MET cc_start: 0.5990 (tmt) cc_final: 0.5482 (mpm) REVERT: A 692 LEU cc_start: 0.7120 (mp) cc_final: 0.6919 (mm) REVERT: A 707 ARG cc_start: 0.7397 (tpp80) cc_final: 0.6855 (mmm160) REVERT: A 713 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8119 (mmm) REVERT: A 738 LYS cc_start: 0.7194 (mtpm) cc_final: 0.6007 (mmtp) REVERT: A 753 MET cc_start: 0.8670 (mmt) cc_final: 0.8154 (mmt) outliers start: 32 outliers final: 23 residues processed: 171 average time/residue: 0.3656 time to fit residues: 69.2259 Evaluate side-chains 175 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 158 GLN 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 713 MET 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 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL 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 764 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 122 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3709 r_free = 0.3709 target = 0.153411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120643 restraints weight = 18834.466| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.82 r_work: 0.3109 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.88 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10912 Z= 0.126 Angle : 0.493 6.083 14884 Z= 0.255 Chirality : 0.041 0.155 1710 Planarity : 0.003 0.037 1806 Dihedral : 6.834 58.244 1951 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.92 % Allowed : 20.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.23), residues: 1268 helix: 2.75 (0.20), residues: 584 sheet: 1.18 (0.31), residues: 272 loop : -0.70 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.026 0.002 TYR A 605 PHE 0.019 0.001 PHE A 697 TRP 0.008 0.001 TRP A 106 HIS 0.004 0.001 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10898) covalent geometry : angle 0.49029 / 0.25 (14868) SS BOND : bond 0.00223 / 0.12 ( 8) SS BOND : angle 1.52127 / 1.11 ( 16) hydrogen bonds : bond 0.03883 / 2.59 ( 634) hydrogen bonds : angle 4.41328 / 3.14 ( 1822) metal coordination : bond 0.00642 / 0.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3873.25 seconds wall clock time: 66 minutes 47.34 seconds (4007.34 seconds total)