Starting phenix.real_space_refine on Thu Aug 6 03:57:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xc1_38236/08_2026/8xc1_38236.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xc1_38236/08_2026/8xc1_38236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xc1_38236/08_2026/8xc1_38236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xc1_38236/08_2026/8xc1_38236.map" model { file = "/net/cci-nas-00/data/ceres_data/8xc1_38236/08_2026/8xc1_38236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xc1_38236/08_2026/8xc1_38236.cif" } resolution = 2.21 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= 0.102 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 P 122 5.49 5 S 68 5.16 5 C 8346 2.51 5 N 2224 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13542 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5257 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 654 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 625 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "B" Number of atoms: 5257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5257 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 654 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "F" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 625 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.69, per 1000 atoms: 0.20 Number of scatterers: 13542 At special positions: 0 Unit cell: (120.157, 111.497, 130.982, 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 68 16.00 P 122 15.00 O 2780 8.00 N 2224 7.00 C 8346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 731 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 423.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 48.9% alpha, 14.7% beta 28 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.732A pdb=" N SER A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.814A pdb=" N GLY A 132 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.903A pdb=" N ASP A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.913A pdb=" N ALA A 471 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 485 removed outlier: 3.622A pdb=" N ILE A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 504 removed outlier: 3.660A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.806A pdb=" N GLN A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 596 removed outlier: 3.692A pdb=" N ASN A 580 " --> pdb=" O PRO A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 626 Processing helix chain 'A' and resid 631 through 652 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 660 through 684 Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.846A pdb=" N GLN A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 738 through 761 Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.732A pdb=" N SER B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.814A pdb=" N GLY B 132 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 314 through 327 Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.904A pdb=" N ASP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.913A pdb=" N ALA B 471 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 485 removed outlier: 3.622A pdb=" N ILE B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 504 removed outlier: 3.660A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 Processing helix chain 'B' and resid 552 through 569 removed outlier: 3.806A pdb=" N GLN B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 596 removed outlier: 3.691A pdb=" N ASN B 580 " --> pdb=" O PRO B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 626 Processing helix chain 'B' and resid 631 through 652 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 660 through 684 Processing helix chain 'B' and resid 689 through 712 removed outlier: 3.846A pdb=" N GLN B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 738 through 761 Processing helix chain 'B' and resid 762 through 766 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.918A pdb=" N THR A 72 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.700A pdb=" N GLN A 213 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 205 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 39 Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.918A pdb=" N THR B 72 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 188 removed outlier: 3.700A pdb=" N GLN B 213 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 205 588 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2093 1.33 - 1.45: 4350 1.45 - 1.57: 7315 1.57 - 1.69: 240 1.69 - 1.81: 102 Bond restraints: 14100 Sorted by residual: bond pdb=" CA ARG B 240 " pdb=" CB ARG B 240 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" CA ARG A 240 " pdb=" CB ARG A 240 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" CD ARG B 240 " pdb=" NE ARG B 240 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.74e+01 bond pdb=" CD ARG A 240 " pdb=" NE ARG A 240 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.74e+01 bond pdb=" O3' G E 9 " pdb=" P A E 10 " ideal model delta sigma weight residual 1.607 1.562 0.045 1.20e-02 6.94e+03 1.42e+01 ... (remaining 14095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.84: 19653 7.84 - 15.67: 27 15.67 - 23.51: 17 23.51 - 31.34: 3 31.34 - 39.18: 4 Bond angle restraints: 19704 Sorted by residual: angle pdb=" N ALA A 133 " pdb=" CA ALA A 133 " pdb=" C ALA A 133 " ideal model delta sigma weight residual 112.87 152.05 -39.18 1.20e+00 6.94e-01 1.07e+03 angle pdb=" N ALA B 133 " pdb=" CA ALA B 133 " pdb=" C ALA B 133 " ideal model delta sigma weight residual 112.87 152.05 -39.18 1.20e+00 6.94e-01 1.07e+03 angle pdb=" C SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta sigma weight residual 110.74 75.84 34.90 1.61e+00 3.86e-01 4.70e+02 angle pdb=" C SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta sigma weight residual 110.74 75.84 34.90 1.61e+00 3.86e-01 4.70e+02 angle pdb=" C ILE B 243 " pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta sigma weight residual 111.88 132.49 -20.61 1.28e+00 6.10e-01 2.59e+02 ... (remaining 19699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 8258 35.50 - 71.01: 684 71.01 - 106.51: 116 106.51 - 142.01: 30 142.01 - 177.51: 8 Dihedral angle restraints: 9096 sinusoidal: 5210 harmonic: 3886 Sorted by residual: dihedral pdb=" C SER B 244 " pdb=" N SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta harmonic sigma weight residual -122.60 -75.99 -46.61 0 2.50e+00 1.60e-01 3.48e+02 dihedral pdb=" C SER A 244 " pdb=" N SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta harmonic sigma weight residual -122.60 -75.99 -46.61 0 2.50e+00 1.60e-01 3.48e+02 dihedral pdb=" C ILE B 243 " pdb=" N ILE B 243 " pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta harmonic sigma weight residual -122.00 -164.90 42.90 0 2.50e+00 1.60e-01 2.94e+02 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 2390 0.334 - 0.669: 13 0.669 - 1.003: 3 1.003 - 1.338: 0 1.338 - 1.672: 4 Chirality restraints: 2410 Sorted by residual: chirality pdb=" CA ILE B 243 " pdb=" N ILE B 243 " pdb=" C ILE B 243 " pdb=" CB ILE B 243 " both_signs ideal model delta sigma weight residual False 2.43 0.76 1.67 2.00e-01 2.50e+01 6.99e+01 chirality pdb=" CA ILE A 243 " pdb=" N ILE A 243 " pdb=" C ILE A 243 " pdb=" CB ILE A 243 " both_signs ideal model delta sigma weight residual False 2.43 0.76 1.67 2.00e-01 2.50e+01 6.99e+01 chirality pdb=" CA ALA B 133 " pdb=" N ALA B 133 " pdb=" C ALA B 133 " pdb=" CB ALA B 133 " both_signs ideal model delta sigma weight residual False 2.48 1.07 1.41 2.00e-01 2.50e+01 4.99e+01 ... (remaining 2407 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 807 " -0.168 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG B 807 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B 807 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG B 807 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG B 807 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 807 " -0.168 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG A 807 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG A 807 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG A 807 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG A 807 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 142 " 0.080 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO B 143 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " 0.060 5.00e-02 4.00e+02 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 62 2.47 - 3.08: 8618 3.08 - 3.69: 21014 3.69 - 4.29: 32120 4.29 - 4.90: 50367 Nonbonded interactions: 112181 Sorted by model distance: nonbonded pdb=" O SER A 244 " pdb=" CB SER A 244 " model vdw 1.869 2.752 nonbonded pdb=" O SER B 244 " pdb=" CB SER B 244 " model vdw 1.869 2.752 nonbonded pdb=" O HIS B 138 " pdb=" CB HIS B 138 " model vdw 2.186 2.752 nonbonded pdb=" O2' C E 11 " pdb=" O5' G E 12 " model vdw 2.257 3.040 nonbonded pdb=" O2' C C 11 " pdb=" O5' G C 12 " model vdw 2.257 3.040 ... (remaining 112176 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.004 0.103 14116 Z= 0.241 Angle : 1.232 39.176 19728 Z= 0.828 Chirality : 0.095 1.672 2410 Planarity : 0.008 0.139 1946 Dihedral : 24.883 177.515 6546 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.05 % Allowed : 23.55 % Favored : 74.40 % Cbeta Deviations : 1.66 % Peptide Plane: Cis-proline : 5.56 % 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: 1.19 (0.24), residues: 1308 helix: 2.42 (0.22), residues: 532 sheet: 1.94 (0.32), residues: 264 loop : -1.79 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 240 TYR 0.019 0.001 TYR A 650 PHE 0.012 0.001 PHE A 103 TRP 0.008 0.001 TRP B 567 HIS 0.003 0.001 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.24 (14100) covalent geometry : angle 1.22874 / 0.83 (19704) SS BOND : bond 0.00107 / 0.05 ( 6) SS BOND : angle 0.41521 / 0.25 ( 12) hydrogen bonds : bond 0.15622 / 9.57 ( 658) hydrogen bonds : angle 5.26331 / 3.64 ( 1776) metal coordination : bond 0.00183 / 0.09 ( 6) link_BETA1-4 : bond 0.01495 / 0.75 ( 4) link_BETA1-4 : angle 4.19722 / 2.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8179 (tp30) REVERT: A 272 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7901 (mtmm) REVERT: B 221 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8195 (tp30) REVERT: B 272 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7899 (mtmm) REVERT: B 604 PHE cc_start: 0.8417 (m-80) cc_final: 0.8208 (m-80) outliers start: 24 outliers final: 17 residues processed: 155 average time/residue: 0.4207 time to fit residues: 72.5583 Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS A 210 ASN A 215 HIS A 227 ASN A 450 HIS B 138 HIS B 210 ASN B 215 HIS B 227 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.181019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113435 restraints weight = 13911.297| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.20 r_work: 0.3208 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14116 Z= 0.233 Angle : 0.750 9.723 19728 Z= 0.390 Chirality : 0.050 0.374 2410 Planarity : 0.006 0.074 1946 Dihedral : 24.936 177.229 4154 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.29 % Allowed : 19.37 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.81 (0.23), residues: 1308 helix: 2.03 (0.22), residues: 546 sheet: 1.68 (0.32), residues: 262 loop : -1.94 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 100 TYR 0.022 0.002 TYR A 650 PHE 0.023 0.002 PHE B 528 TRP 0.009 0.002 TRP A 567 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (14100) covalent geometry : angle 0.74263 / 0.39 (19704) SS BOND : bond 0.00248 / 0.12 ( 6) SS BOND : angle 0.76653 / 0.48 ( 12) hydrogen bonds : bond 0.06807 / 4.48 ( 658) hydrogen bonds : angle 4.61681 / 3.23 ( 1776) metal coordination : bond 0.00529 / 0.27 ( 6) link_BETA1-4 : bond 0.01108 / 0.56 ( 4) link_BETA1-4 : angle 4.38000 / 2.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 131 time to evaluate : 0.427 Fit side-chains REVERT: A 221 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8344 (tp30) REVERT: A 246 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6200 (ptpp) REVERT: A 432 GLN cc_start: 0.7525 (mt0) cc_final: 0.7132 (tt0) REVERT: B 221 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8361 (tp30) REVERT: B 246 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6208 (ptpp) REVERT: B 432 GLN cc_start: 0.7382 (mt0) cc_final: 0.7134 (tt0) outliers start: 62 outliers final: 38 residues processed: 170 average time/residue: 0.4230 time to fit residues: 80.2643 Evaluate side-chains 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.182838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114218 restraints weight = 13972.267| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.19 r_work: 0.3274 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14116 Z= 0.135 Angle : 0.638 9.403 19728 Z= 0.326 Chirality : 0.044 0.344 2410 Planarity : 0.005 0.065 1946 Dihedral : 23.281 173.417 4146 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.18 % Allowed : 19.97 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.19 (0.23), residues: 1308 helix: 2.28 (0.22), residues: 548 sheet: 1.83 (0.32), residues: 262 loop : -1.64 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.022 0.002 TYR A 650 PHE 0.013 0.001 PHE A 103 TRP 0.006 0.001 TRP A 567 HIS 0.003 0.001 HIS A 740 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (14100) covalent geometry : angle 0.62874 / 0.32 (19704) SS BOND : bond 0.00073 / 0.03 ( 6) SS BOND : angle 0.30875 / 0.20 ( 12) hydrogen bonds : bond 0.05489 / 3.57 ( 658) hydrogen bonds : angle 4.40423 / 3.08 ( 1776) metal coordination : bond 0.00275 / 0.14 ( 6) link_BETA1-4 : bond 0.01443 / 0.73 ( 4) link_BETA1-4 : angle 4.49993 / 2.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.429 Fit side-chains REVERT: A 246 LYS cc_start: 0.6356 (OUTLIER) cc_final: 0.6079 (pmtt) REVERT: A 272 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7775 (mtmm) REVERT: A 430 MET cc_start: 0.6668 (mtp) cc_final: 0.6465 (mtp) REVERT: A 432 GLN cc_start: 0.7282 (mt0) cc_final: 0.7045 (tt0) REVERT: B 272 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7778 (mtmm) outliers start: 49 outliers final: 24 residues processed: 162 average time/residue: 0.4943 time to fit residues: 89.1214 Evaluate side-chains 154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 100 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 71 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 69 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.182181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112872 restraints weight = 13946.782| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.35 r_work: 0.3243 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14116 Z= 0.145 Angle : 0.638 9.915 19728 Z= 0.325 Chirality : 0.044 0.339 2410 Planarity : 0.004 0.069 1946 Dihedral : 22.222 171.626 4140 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.69 % Allowed : 19.54 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.23 (0.23), residues: 1308 helix: 2.34 (0.22), residues: 548 sheet: 1.81 (0.32), residues: 262 loop : -1.64 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.023 0.002 TYR B 650 PHE 0.016 0.001 PHE B 528 TRP 0.008 0.001 TRP A 567 HIS 0.003 0.001 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (14100) covalent geometry : angle 0.62658 / 0.32 (19704) SS BOND : bond 0.00107 / 0.05 ( 6) SS BOND : angle 0.44114 / 0.28 ( 12) hydrogen bonds : bond 0.05481 / 3.60 ( 658) hydrogen bonds : angle 4.32177 / 3.02 ( 1776) metal coordination : bond 0.00210 / 0.10 ( 6) link_BETA1-4 : bond 0.01418 / 0.72 ( 4) link_BETA1-4 : angle 4.93151 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 136 time to evaluate : 0.536 Fit side-chains REVERT: A 246 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5918 (ptpp) REVERT: A 272 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7850 (mtmm) REVERT: A 430 MET cc_start: 0.6642 (mtp) cc_final: 0.6411 (mtp) REVERT: A 674 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7597 (mp) REVERT: B 272 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7857 (mtmm) REVERT: B 432 GLN cc_start: 0.7189 (mt0) cc_final: 0.6785 (tt0) REVERT: B 674 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7600 (mp) outliers start: 55 outliers final: 26 residues processed: 168 average time/residue: 0.5010 time to fit residues: 93.7294 Evaluate side-chains 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 729 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 5.9990 chunk 36 optimal weight: 0.0470 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 139 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.182064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118408 restraints weight = 13840.739| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.91 r_work: 0.3228 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14116 Z= 0.163 Angle : 0.625 8.313 19728 Z= 0.326 Chirality : 0.044 0.338 2410 Planarity : 0.005 0.071 1946 Dihedral : 21.984 169.329 4138 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.38 % Allowed : 18.86 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.11 (0.23), residues: 1308 helix: 2.29 (0.21), residues: 546 sheet: 1.76 (0.32), residues: 262 loop : -1.76 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.022 0.002 TYR A 650 PHE 0.030 0.002 PHE B 513 TRP 0.006 0.001 TRP A 567 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (14100) covalent geometry : angle 0.61262 / 0.32 (19704) SS BOND : bond 0.00110 / 0.06 ( 6) SS BOND : angle 0.45376 / 0.29 ( 12) hydrogen bonds : bond 0.05815 / 3.83 ( 658) hydrogen bonds : angle 4.38587 / 3.07 ( 1776) metal coordination : bond 0.00283 / 0.13 ( 6) link_BETA1-4 : bond 0.01673 / 0.85 ( 4) link_BETA1-4 : angle 5.10360 / 3.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 133 time to evaluate : 0.457 Fit side-chains REVERT: A 193 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7584 (mtmm) REVERT: A 272 LYS cc_start: 0.8370 (mtpp) cc_final: 0.7905 (mtmm) REVERT: A 430 MET cc_start: 0.6751 (mtp) cc_final: 0.6493 (mtp) REVERT: A 674 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7610 (mp) REVERT: B 193 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7546 (mtmm) REVERT: B 272 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7910 (mtmm) REVERT: B 674 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7608 (mp) outliers start: 63 outliers final: 37 residues processed: 170 average time/residue: 0.4633 time to fit residues: 87.6182 Evaluate side-chains 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.0770 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.0270 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.183083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114620 restraints weight = 13909.806| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.27 r_work: 0.3265 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14116 Z= 0.124 Angle : 0.586 12.344 19728 Z= 0.305 Chirality : 0.042 0.337 2410 Planarity : 0.004 0.069 1946 Dihedral : 21.713 168.782 4134 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.20 % Allowed : 19.37 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.31 (0.24), residues: 1308 helix: 2.47 (0.22), residues: 548 sheet: 1.82 (0.32), residues: 262 loop : -1.66 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.022 0.001 TYR B 650 PHE 0.013 0.001 PHE A 103 TRP 0.007 0.001 TRP A 567 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (14100) covalent geometry : angle 0.57265 / 0.30 (19704) SS BOND : bond 0.00066 / 0.03 ( 6) SS BOND : angle 0.28680 / 0.19 ( 12) hydrogen bonds : bond 0.05230 / 3.43 ( 658) hydrogen bonds : angle 4.29269 / 3.01 ( 1776) metal coordination : bond 0.00177 / 0.09 ( 6) link_BETA1-4 : bond 0.01604 / 0.81 ( 4) link_BETA1-4 : angle 5.05822 / 3.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 134 time to evaluate : 0.430 Fit side-chains REVERT: A 193 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7545 (mtmm) REVERT: A 272 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7783 (mtmm) REVERT: A 430 MET cc_start: 0.6726 (mtp) cc_final: 0.6477 (mtp) REVERT: A 457 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7838 (mmp) REVERT: A 659 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7621 (p0) REVERT: A 674 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7560 (mp) REVERT: B 193 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7520 (mtmm) REVERT: B 272 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7785 (mtmm) REVERT: B 457 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.7830 (mmp) REVERT: B 659 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7635 (p0) REVERT: B 674 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7563 (mp) outliers start: 61 outliers final: 33 residues processed: 172 average time/residue: 0.4854 time to fit residues: 93.1298 Evaluate side-chains 171 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 729 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.182351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113075 restraints weight = 13754.537| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.13 r_work: 0.3254 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14116 Z= 0.155 Angle : 0.611 8.461 19728 Z= 0.317 Chirality : 0.043 0.338 2410 Planarity : 0.004 0.070 1946 Dihedral : 21.586 166.964 4134 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.86 % Allowed : 20.05 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.17 (0.23), residues: 1308 helix: 2.40 (0.21), residues: 546 sheet: 1.72 (0.32), residues: 262 loop : -1.74 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.022 0.002 TYR A 650 PHE 0.018 0.002 PHE B 528 TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14100) covalent geometry : angle 0.59781 / 0.31 (19704) SS BOND : bond 0.00128 / 0.06 ( 6) SS BOND : angle 0.51441 / 0.33 ( 12) hydrogen bonds : bond 0.05686 / 3.74 ( 658) hydrogen bonds : angle 4.34456 / 3.05 ( 1776) metal coordination : bond 0.00308 / 0.15 ( 6) link_BETA1-4 : bond 0.01550 / 0.79 ( 4) link_BETA1-4 : angle 5.14313 / 3.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 137 time to evaluate : 0.407 Fit side-chains REVERT: A 193 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7520 (mtmm) REVERT: A 272 LYS cc_start: 0.8373 (mtpp) cc_final: 0.7918 (mtmm) REVERT: A 307 LYS cc_start: 0.8150 (mttp) cc_final: 0.7938 (mtmt) REVERT: A 430 MET cc_start: 0.6767 (mtp) cc_final: 0.6510 (mtp) REVERT: A 659 ASN cc_start: 0.7910 (p0) cc_final: 0.7651 (p0) REVERT: A 674 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7612 (mp) REVERT: B 193 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7537 (mtmm) REVERT: B 272 LYS cc_start: 0.8376 (mtpp) cc_final: 0.7919 (mtmm) REVERT: B 307 LYS cc_start: 0.8143 (mttp) cc_final: 0.7930 (mtmt) REVERT: B 457 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7854 (mmp) REVERT: B 659 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7647 (p0) REVERT: B 674 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7615 (mp) outliers start: 57 outliers final: 34 residues processed: 172 average time/residue: 0.4612 time to fit residues: 88.5907 Evaluate side-chains 174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.180238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109860 restraints weight = 13566.729| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.36 r_work: 0.3205 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14116 Z= 0.235 Angle : 0.693 8.927 19728 Z= 0.356 Chirality : 0.047 0.339 2410 Planarity : 0.005 0.067 1946 Dihedral : 21.698 165.310 4134 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.52 % Allowed : 20.14 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.80 (0.23), residues: 1308 helix: 2.05 (0.21), residues: 546 sheet: 1.51 (0.32), residues: 262 loop : -1.88 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 570 TYR 0.021 0.002 TYR A 650 PHE 0.024 0.002 PHE B 528 TRP 0.005 0.002 TRP A 743 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (14100) covalent geometry : angle 0.67933 / 0.35 (19704) SS BOND : bond 0.00267 / 0.13 ( 6) SS BOND : angle 0.84222 / 0.54 ( 12) hydrogen bonds : bond 0.06709 / 4.45 ( 658) hydrogen bonds : angle 4.54271 / 3.18 ( 1776) metal coordination : bond 0.00627 / 0.29 ( 6) link_BETA1-4 : bond 0.01346 / 0.68 ( 4) link_BETA1-4 : angle 5.50817 / 3.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 0.338 Fit side-chains REVERT: A 193 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7625 (mtmm) REVERT: A 272 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8022 (mtmm) REVERT: A 674 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 193 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7616 (mtmm) REVERT: B 674 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7620 (mp) outliers start: 53 outliers final: 37 residues processed: 169 average time/residue: 0.4612 time to fit residues: 87.2962 Evaluate side-chains 171 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 99 optimal weight: 0.0070 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.183204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115336 restraints weight = 13739.125| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.21 r_work: 0.3238 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14116 Z= 0.129 Angle : 0.571 8.360 19728 Z= 0.299 Chirality : 0.042 0.344 2410 Planarity : 0.004 0.066 1946 Dihedral : 21.489 165.533 4134 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.50 % Allowed : 21.42 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.20 (0.23), residues: 1308 helix: 2.38 (0.21), residues: 548 sheet: 1.73 (0.32), residues: 262 loop : -1.71 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 570 TYR 0.022 0.001 TYR A 650 PHE 0.012 0.001 PHE A 103 TRP 0.007 0.001 TRP A 567 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (14100) covalent geometry : angle 0.55763 / 0.30 (19704) SS BOND : bond 0.00034 / 0.02 ( 6) SS BOND : angle 0.24234 / 0.15 ( 12) hydrogen bonds : bond 0.05350 / 3.50 ( 658) hydrogen bonds : angle 4.32292 / 3.03 ( 1776) metal coordination : bond 0.00265 / 0.14 ( 6) link_BETA1-4 : bond 0.01576 / 0.79 ( 4) link_BETA1-4 : angle 5.01896 / 3.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.320 Fit side-chains REVERT: A 193 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7474 (mtmm) REVERT: A 430 MET cc_start: 0.6899 (mtp) cc_final: 0.6681 (mtp) REVERT: A 457 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7799 (mmp) REVERT: A 659 ASN cc_start: 0.7802 (p0) cc_final: 0.7575 (p0) REVERT: A 674 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7470 (mp) REVERT: B 193 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7496 (mtmm) REVERT: B 659 ASN cc_start: 0.7778 (p0) cc_final: 0.7550 (p0) REVERT: B 674 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7471 (mp) outliers start: 41 outliers final: 26 residues processed: 158 average time/residue: 0.4744 time to fit residues: 83.6048 Evaluate side-chains 157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 50.0000 chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.183246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.113856 restraints weight = 13628.792| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.28 r_work: 0.3249 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14116 Z= 0.134 Angle : 0.579 8.247 19728 Z= 0.301 Chirality : 0.042 0.344 2410 Planarity : 0.004 0.069 1946 Dihedral : 21.346 165.592 4134 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.82 % Allowed : 22.35 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.26 (0.23), residues: 1308 helix: 2.46 (0.22), residues: 548 sheet: 1.74 (0.32), residues: 262 loop : -1.68 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.022 0.002 TYR B 650 PHE 0.020 0.001 PHE B 513 TRP 0.008 0.001 TRP B 567 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14100) covalent geometry : angle 0.56622 / 0.30 (19704) SS BOND : bond 0.00126 / 0.06 ( 6) SS BOND : angle 0.41866 / 0.26 ( 12) hydrogen bonds : bond 0.05314 / 3.48 ( 658) hydrogen bonds : angle 4.30587 / 3.02 ( 1776) metal coordination : bond 0.00256 / 0.12 ( 6) link_BETA1-4 : bond 0.01373 / 0.69 ( 4) link_BETA1-4 : angle 4.99525 / 3.14 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.403 Fit side-chains REVERT: A 193 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7583 (mtmm) REVERT: A 272 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7851 (mtmm) REVERT: A 659 ASN cc_start: 0.7883 (p0) cc_final: 0.7670 (p0) REVERT: A 674 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7574 (mp) REVERT: B 193 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7573 (mtmm) REVERT: B 272 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7832 (mtmm) REVERT: B 659 ASN cc_start: 0.7864 (p0) cc_final: 0.7630 (p0) REVERT: B 674 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7582 (mp) outliers start: 33 outliers final: 26 residues processed: 152 average time/residue: 0.4255 time to fit residues: 72.2307 Evaluate side-chains 156 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.182701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114751 restraints weight = 13598.804| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.15 r_work: 0.3233 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14116 Z= 0.151 Angle : 0.593 8.345 19728 Z= 0.306 Chirality : 0.042 0.346 2410 Planarity : 0.004 0.068 1946 Dihedral : 21.287 165.478 4134 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.16 % Allowed : 22.18 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.18 (0.23), residues: 1308 helix: 2.40 (0.21), residues: 546 sheet: 1.72 (0.33), residues: 262 loop : -1.74 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.021 0.002 TYR B 650 PHE 0.016 0.002 PHE B 528 TRP 0.007 0.001 TRP A 567 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14100) covalent geometry : angle 0.58037 / 0.30 (19704) SS BOND : bond 0.00145 / 0.07 ( 6) SS BOND : angle 0.38675 / 0.25 ( 12) hydrogen bonds : bond 0.05571 / 3.66 ( 658) hydrogen bonds : angle 4.35238 / 3.05 ( 1776) metal coordination : bond 0.00294 / 0.15 ( 6) link_BETA1-4 : bond 0.01386 / 0.70 ( 4) link_BETA1-4 : angle 5.01153 / 3.14 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6569.76 seconds wall clock time: 112 minutes 21.68 seconds (6741.68 seconds total)