Starting phenix.real_space_refine on Sat Aug 23 16:42:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xc1_38236/08_2025/8xc1_38236.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xc1_38236/08_2025/8xc1_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_2025/8xc1_38236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xc1_38236/08_2025/8xc1_38236.map" model { file = "/net/cci-nas-00/data/ceres_data/8xc1_38236/08_2025/8xc1_38236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xc1_38236/08_2025/8xc1_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-2.0-5787/lib/python3.9/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: 3.82, per 1000 atoms: 0.28 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: 1.13 Conformation dependent library (CDL) restraints added in 599.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.83 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: 2.78 Time building geometry restraints manager: 1.55 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=" N PRO B 143 " pdb=" CD PRO B 143 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.33e+01 ... (remaining 14095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.84: 19651 7.84 - 15.67: 29 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: 2388 0.334 - 0.669: 15 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: 0.02 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: 1.720 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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= 0.208 Angle : 1.197 39.176 19728 Z= 0.732 Chirality : 0.091 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 aren 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 covalent geometry : bond 0.00397 (14100) covalent geometry : angle 1.19370 (19704) SS BOND : bond 0.00107 ( 6) SS BOND : angle 0.41521 ( 12) hydrogen bonds : bond 0.15622 ( 658) hydrogen bonds : angle 5.26331 ( 1776) metal coordination : bond 0.00183 ( 6) link_BETA1-4 : bond 0.01495 ( 4) link_BETA1-4 : angle 4.19722 ( 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 : 0.524 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: 0.5830 time to fit residues: 99.6410 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 : 0.490 ------------------------------------------------------------------------------- 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: 30.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4194 r_free = 0.4194 target = 0.180732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110805 restraints weight = 13868.827| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.22 r_work: 0.3237 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14116 Z= 0.238 Angle : 0.787 9.461 19728 Z= 0.386 Chirality : 0.048 0.236 2410 Planarity : 0.006 0.073 1946 Dihedral : 24.489 175.233 4154 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.67 % Favored : 96.18 % Rotamer: Outliers : 5.72 % Allowed : 19.45 % 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 aren not related in a simple way. whole: 0.88 (0.23), residues: 1308 helix: 2.00 (0.22), residues: 546 sheet: 1.69 (0.33), residues: 262 loop : -1.78 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 570 TYR 0.022 0.002 TYR B 650 PHE 0.022 0.002 PHE A 528 TRP 0.008 0.002 TRP B 567 HIS 0.007 0.002 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00542 (14100) covalent geometry : angle 0.77889 (19704) SS BOND : bond 0.00223 ( 6) SS BOND : angle 0.73190 ( 12) hydrogen bonds : bond 0.06513 ( 658) hydrogen bonds : angle 4.58289 ( 1776) metal coordination : bond 0.00472 ( 6) link_BETA1-4 : bond 0.01200 ( 4) link_BETA1-4 : angle 4.70593 ( 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 201 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 134 time to evaluate : 0.461 Fit side-chains REVERT: A 221 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8493 (tp30) REVERT: A 246 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6031 (ptpp) REVERT: A 430 MET cc_start: 0.6741 (mtp) cc_final: 0.6503 (mtp) REVERT: B 116 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8974 (mp) REVERT: B 221 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8504 (tp30) REVERT: B 246 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6043 (ptpp) REVERT: B 430 MET cc_start: 0.6743 (mtp) cc_final: 0.6505 (mtp) outliers start: 67 outliers final: 37 residues processed: 177 average time/residue: 0.5095 time to fit residues: 100.4996 Evaluate side-chains 170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 116 LEU 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 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 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: 0.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.183536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114697 restraints weight = 13985.270| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.29 r_work: 0.3270 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1273 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= 0.129 Angle : 0.662 9.242 19728 Z= 0.320 Chirality : 0.042 0.236 2410 Planarity : 0.004 0.063 1946 Dihedral : 22.725 171.329 4146 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.92 % Allowed : 20.39 % Favored : 75.68 % 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 aren not related in a simple way. whole: 1.28 (0.24), residues: 1308 helix: 2.37 (0.22), residues: 548 sheet: 1.90 (0.32), residues: 264 loop : -1.65 (0.26), residues: 496 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 0.016 0.001 PHE A 513 TRP 0.006 0.001 TRP A 567 HIS 0.004 0.001 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00262 (14100) covalent geometry : angle 0.65178 (19704) SS BOND : bond 0.00102 ( 6) SS BOND : angle 0.23943 ( 12) hydrogen bonds : bond 0.04848 ( 658) hydrogen bonds : angle 4.31866 ( 1776) metal coordination : bond 0.00271 ( 6) link_BETA1-4 : bond 0.01532 ( 4) link_BETA1-4 : angle 4.72917 ( 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 178 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.482 Fit side-chains REVERT: A 246 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5972 (ptpp) REVERT: A 430 MET cc_start: 0.6659 (mtp) cc_final: 0.6400 (mtp) REVERT: B 246 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.5981 (ptpp) REVERT: B 430 MET cc_start: 0.6643 (mtp) cc_final: 0.6385 (mtp) outliers start: 46 outliers final: 16 residues processed: 159 average time/residue: 0.5798 time to fit residues: 101.4298 Evaluate side-chains 140 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 515 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 674 LEU 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 246 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 580 ASN B 432 GLN B 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.180661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111588 restraints weight = 13799.852| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.30 r_work: 0.3211 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14116 Z= 0.220 Angle : 0.723 8.717 19728 Z= 0.357 Chirality : 0.045 0.218 2410 Planarity : 0.005 0.067 1946 Dihedral : 22.354 166.729 4142 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.95 % Allowed : 19.20 % 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 aren not related in a simple way. whole: 0.90 (0.23), residues: 1308 helix: 2.10 (0.21), residues: 546 sheet: 1.70 (0.33), residues: 262 loop : -1.88 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 570 TYR 0.023 0.002 TYR A 650 PHE 0.023 0.002 PHE A 528 TRP 0.006 0.002 TRP A 567 HIS 0.006 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00502 (14100) covalent geometry : angle 0.71172 (19704) SS BOND : bond 0.00225 ( 6) SS BOND : angle 0.74961 ( 12) hydrogen bonds : bond 0.06247 ( 658) hydrogen bonds : angle 4.49415 ( 1776) metal coordination : bond 0.00496 ( 6) link_BETA1-4 : bond 0.01314 ( 4) link_BETA1-4 : angle 5.12976 ( 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 186 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.483 Fit side-chains REVERT: A 246 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5862 (ptpp) REVERT: A 659 ASN cc_start: 0.7862 (p0) cc_final: 0.7652 (p0) REVERT: A 674 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7560 (mp) REVERT: B 246 LYS cc_start: 0.6266 (OUTLIER) cc_final: 0.5893 (ptpp) REVERT: B 674 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7563 (mp) outliers start: 58 outliers final: 33 residues processed: 167 average time/residue: 0.5163 time to fit residues: 96.0195 Evaluate side-chains 164 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 ILE 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 280 ILE Chi-restraints excluded: chain A residue 332 PHE 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 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 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU 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 246 LYS 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 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 674 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.183124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115171 restraints weight = 13777.649| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.17 r_work: 0.3277 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1612 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= 0.137 Angle : 0.626 8.460 19728 Z= 0.311 Chirality : 0.042 0.241 2410 Planarity : 0.004 0.065 1946 Dihedral : 21.897 165.905 4142 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.27 % Allowed : 20.48 % Favored : 75.26 % 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 aren not related in a simple way. whole: 1.15 (0.23), residues: 1308 helix: 2.34 (0.22), residues: 548 sheet: 1.82 (0.32), residues: 262 loop : -1.81 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.023 0.001 TYR A 650 PHE 0.014 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 covalent geometry : bond 0.00288 (14100) covalent geometry : angle 0.61379 (19704) SS BOND : bond 0.00082 ( 6) SS BOND : angle 0.29992 ( 12) hydrogen bonds : bond 0.05005 ( 658) hydrogen bonds : angle 4.29946 ( 1776) metal coordination : bond 0.00204 ( 6) link_BETA1-4 : bond 0.01651 ( 4) link_BETA1-4 : angle 5.05217 ( 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 179 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 129 time to evaluate : 0.405 Fit side-chains REVERT: A 430 MET cc_start: 0.6907 (mtp) cc_final: 0.6675 (mtp) REVERT: A 659 ASN cc_start: 0.7861 (p0) cc_final: 0.7639 (p0) REVERT: A 674 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 246 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5904 (ptpp) REVERT: B 430 MET cc_start: 0.6913 (mtp) cc_final: 0.6680 (mtp) REVERT: B 674 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7628 (mp) outliers start: 50 outliers final: 26 residues processed: 163 average time/residue: 0.5197 time to fit residues: 93.9824 Evaluate side-chains 154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 674 LEU Chi-restraints excluded: chain A residue 684 HIS 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 246 LYS 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 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 729 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.0050 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.180686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111437 restraints weight = 13722.013| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.09 r_work: 0.3222 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14116 Z= 0.217 Angle : 0.713 9.158 19728 Z= 0.353 Chirality : 0.045 0.225 2410 Planarity : 0.004 0.066 1946 Dihedral : 21.909 163.953 4138 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.86 % Allowed : 20.22 % Favored : 74.91 % 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 aren not related in a simple way. whole: 0.86 (0.23), residues: 1308 helix: 2.15 (0.21), residues: 546 sheet: 1.61 (0.32), residues: 262 loop : -1.97 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 570 TYR 0.022 0.002 TYR B 650 PHE 0.023 0.002 PHE A 528 TRP 0.006 0.002 TRP A 567 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00496 (14100) covalent geometry : angle 0.70131 (19704) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.74025 ( 12) hydrogen bonds : bond 0.06198 ( 658) hydrogen bonds : angle 4.48108 ( 1776) metal coordination : bond 0.00559 ( 6) link_BETA1-4 : bond 0.01375 ( 4) link_BETA1-4 : angle 5.33238 ( 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 182 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 125 time to evaluate : 0.530 Fit side-chains REVERT: A 430 MET cc_start: 0.6795 (mtp) cc_final: 0.6570 (mtp) REVERT: A 674 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7584 (mp) REVERT: B 246 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.5896 (ptpp) REVERT: B 430 MET cc_start: 0.6798 (mtp) cc_final: 0.6574 (mtp) REVERT: B 674 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7588 (mp) outliers start: 57 outliers final: 37 residues processed: 165 average time/residue: 0.4998 time to fit residues: 92.2421 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 : 0.454 ------------------------------------------------------------------------------- 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 197 VAL Chi-restraints excluded: chain A residue 200 ILE 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 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 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU 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 246 LYS 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 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 674 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.0270 chunk 54 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS B 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.182377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113521 restraints weight = 13659.769| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.08 r_work: 0.3255 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14116 Z= 0.152 Angle : 0.640 8.501 19728 Z= 0.316 Chirality : 0.042 0.253 2410 Planarity : 0.004 0.069 1946 Dihedral : 21.679 163.363 4138 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.69 % Allowed : 20.39 % Favored : 74.91 % 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 aren not related in a simple way. whole: 1.05 (0.23), residues: 1308 helix: 2.32 (0.21), residues: 546 sheet: 1.69 (0.32), residues: 262 loop : -1.89 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.023 0.002 TYR B 650 PHE 0.014 0.001 PHE A 103 TRP 0.008 0.001 TRP A 567 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00331 (14100) covalent geometry : angle 0.62755 (19704) SS BOND : bond 0.00162 ( 6) SS BOND : angle 0.46988 ( 12) hydrogen bonds : bond 0.05282 ( 658) hydrogen bonds : angle 4.33560 ( 1776) metal coordination : bond 0.00221 ( 6) link_BETA1-4 : bond 0.01469 ( 4) link_BETA1-4 : angle 5.05593 ( 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 187 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 0.512 Fit side-chains REVERT: A 272 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7831 (mtmm) REVERT: A 430 MET cc_start: 0.6748 (mtp) cc_final: 0.6538 (mtp) REVERT: A 674 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7608 (mp) REVERT: B 246 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5986 (ptpp) REVERT: B 272 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7830 (mtmm) REVERT: B 430 MET cc_start: 0.6772 (mtp) cc_final: 0.6556 (mtp) REVERT: B 674 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7608 (mp) outliers start: 55 outliers final: 35 residues processed: 169 average time/residue: 0.5374 time to fit residues: 101.0001 Evaluate side-chains 167 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 VAL 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 674 LEU Chi-restraints excluded: chain A residue 684 HIS 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 231 VAL Chi-restraints excluded: chain B residue 246 LYS 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 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 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: 6.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.180858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112720 restraints weight = 13508.596| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.02 r_work: 0.3232 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14116 Z= 0.205 Angle : 0.697 8.625 19728 Z= 0.344 Chirality : 0.044 0.237 2410 Planarity : 0.004 0.067 1946 Dihedral : 21.720 164.004 4138 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.61 % Allowed : 20.48 % Favored : 74.91 % 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 aren not related in a simple way. whole: 0.86 (0.23), residues: 1308 helix: 2.16 (0.21), residues: 546 sheet: 1.56 (0.32), residues: 262 loop : -1.95 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 570 TYR 0.021 0.002 TYR A 650 PHE 0.022 0.002 PHE B 528 TRP 0.006 0.002 TRP B 567 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00467 (14100) covalent geometry : angle 0.68508 (19704) SS BOND : bond 0.00201 ( 6) SS BOND : angle 0.74885 ( 12) hydrogen bonds : bond 0.06104 ( 658) hydrogen bonds : angle 4.46317 ( 1776) metal coordination : bond 0.00389 ( 6) link_BETA1-4 : bond 0.01418 ( 4) link_BETA1-4 : angle 5.23765 ( 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 182 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.470 Fit side-chains REVERT: A 674 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7552 (mp) REVERT: B 246 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5993 (ptpp) REVERT: B 674 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7548 (mp) outliers start: 54 outliers final: 38 residues processed: 169 average time/residue: 0.4696 time to fit residues: 88.5349 Evaluate side-chains 168 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 197 VAL Chi-restraints excluded: chain A residue 200 ILE 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 512 VAL 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 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 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 197 VAL 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 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 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 674 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.182778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113865 restraints weight = 13670.519| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.15 r_work: 0.3259 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14116 Z= 0.143 Angle : 0.626 8.090 19728 Z= 0.310 Chirality : 0.041 0.247 2410 Planarity : 0.004 0.070 1946 Dihedral : 21.524 163.654 4138 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.84 % Allowed : 21.08 % 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 aren not related in a simple way. whole: 1.10 (0.23), residues: 1308 helix: 2.36 (0.21), residues: 546 sheet: 1.73 (0.32), residues: 264 loop : -1.87 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.023 0.001 TYR B 650 PHE 0.014 0.001 PHE A 103 TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00312 (14100) covalent geometry : angle 0.61475 (19704) SS BOND : bond 0.00119 ( 6) SS BOND : angle 0.36070 ( 12) hydrogen bonds : bond 0.05158 ( 658) hydrogen bonds : angle 4.32738 ( 1776) metal coordination : bond 0.00247 ( 6) link_BETA1-4 : bond 0.01358 ( 4) link_BETA1-4 : angle 4.93989 ( 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 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.471 Fit side-chains REVERT: A 272 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7764 (mtmm) REVERT: A 674 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7590 (mp) REVERT: B 246 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.6020 (ptpp) REVERT: B 272 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7760 (mtmm) REVERT: B 674 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7592 (mp) outliers start: 45 outliers final: 36 residues processed: 163 average time/residue: 0.4943 time to fit residues: 89.8254 Evaluate side-chains 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 VAL 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 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 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 246 LYS 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 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 658 LEU Chi-restraints excluded: chain B residue 674 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 30.0000 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS B 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.181348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115248 restraints weight = 13562.009| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.01 r_work: 0.3213 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14116 Z= 0.191 Angle : 0.678 8.321 19728 Z= 0.335 Chirality : 0.043 0.249 2410 Planarity : 0.004 0.068 1946 Dihedral : 21.502 164.320 4138 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.33 % Allowed : 22.01 % 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 aren not related in a simple way. whole: 0.91 (0.23), residues: 1308 helix: 2.21 (0.21), residues: 546 sheet: 1.58 (0.33), residues: 262 loop : -1.92 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 570 TYR 0.022 0.002 TYR B 650 PHE 0.021 0.002 PHE B 528 TRP 0.007 0.001 TRP A 567 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00432 (14100) covalent geometry : angle 0.66690 (19704) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.70029 ( 12) hydrogen bonds : bond 0.05874 ( 658) hydrogen bonds : angle 4.44749 ( 1776) metal coordination : bond 0.00435 ( 6) link_BETA1-4 : bond 0.01310 ( 4) link_BETA1-4 : angle 5.08470 ( 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 166 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.284 Fit side-chains REVERT: A 272 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7867 (mtmm) REVERT: A 674 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7584 (mp) REVERT: B 246 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6232 (ptpp) REVERT: B 272 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7858 (mtmm) REVERT: B 674 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7584 (mp) outliers start: 39 outliers final: 32 residues processed: 158 average time/residue: 0.4797 time to fit residues: 84.4140 Evaluate side-chains 162 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 512 VAL 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 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 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 246 LYS 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 674 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 549 GLN B 450 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.181778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112791 restraints weight = 13592.740| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.20 r_work: 0.3229 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14116 Z= 0.178 Angle : 0.658 8.381 19728 Z= 0.324 Chirality : 0.042 0.250 2410 Planarity : 0.004 0.070 1946 Dihedral : 21.448 164.004 4138 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.58 % Allowed : 21.76 % 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 aren not related in a simple way. whole: 0.93 (0.23), residues: 1308 helix: 2.23 (0.21), residues: 546 sheet: 1.56 (0.32), residues: 262 loop : -1.90 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 570 TYR 0.021 0.002 TYR B 650 PHE 0.018 0.002 PHE B 528 TRP 0.007 0.001 TRP A 567 HIS 0.004 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00402 (14100) covalent geometry : angle 0.64597 (19704) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.45453 ( 12) hydrogen bonds : bond 0.05611 ( 658) hydrogen bonds : angle 4.41155 ( 1776) metal coordination : bond 0.00378 ( 6) link_BETA1-4 : bond 0.01359 ( 4) link_BETA1-4 : angle 5.10114 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8160.97 seconds wall clock time: 139 minutes 20.59 seconds (8360.59 seconds total)