Starting phenix.real_space_refine on Fri Jul 3 09:25:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xc1_38236/07_2026/8xc1_38236.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xc1_38236/07_2026/8xc1_38236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xc1_38236/07_2026/8xc1_38236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xc1_38236/07_2026/8xc1_38236.map" model { file = "/net/cci-nas-00/data/ceres_data/8xc1_38236/07_2026/8xc1_38236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xc1_38236/07_2026/8xc1_38236.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 122 5.49 5 S 68 5.16 5 C 8346 2.51 5 N 2224 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13542 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5257 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 654 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 625 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "B" Number of atoms: 5257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5257 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 654 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "F" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 625 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.77, per 1000 atoms: 0.20 Number of scatterers: 13542 At special positions: 0 Unit cell: (120.157, 111.497, 130.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 68 16.00 P 122 15.00 O 2780 8.00 N 2224 7.00 C 8346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 398.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 48.9% alpha, 14.7% beta 28 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 1.36 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: 1.94 Time building geometry restraints manager: 1.46 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 14116 Z= 0.230 Angle : 1.198 39.176 19728 Z= 0.790 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 are not related in a simple way. whole: 1.19 (0.24), residues: 1308 helix: 2.42 (0.22), residues: 532 sheet: 1.94 (0.32), residues: 264 loop : -1.79 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 240 TYR 0.019 0.001 TYR A 650 PHE 0.012 0.001 PHE A 103 TRP 0.008 0.001 TRP B 567 HIS 0.003 0.001 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.23 (14100) covalent geometry : angle 1.19377 / 0.79 (19704) SS BOND : bond 0.00107 / 0.05 ( 6) SS BOND : angle 0.41521 / 0.25 ( 12) hydrogen bonds : bond 0.15622 / 9.57 ( 658) hydrogen bonds : angle 5.26331 / 3.64 ( 1776) metal coordination : bond 0.00183 / 0.09 ( 6) link_BETA1-4 : bond 0.01495 / 0.75 ( 4) link_BETA1-4 : angle 4.19722 / 2.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.291 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: 0.4252 time to fit residues: 73.3223 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 : 0.397 ------------------------------------------------------------------------------- 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: 40.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS A 210 ASN A 215 HIS A 227 ASN A 450 HIS B 138 HIS B 210 ASN B 215 HIS B 227 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.181145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113422 restraints weight = 13905.365| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.23 r_work: 0.3225 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14116 Z= 0.233 Angle : 0.727 9.436 19728 Z= 0.383 Chirality : 0.048 0.225 2410 Planarity : 0.006 0.074 1946 Dihedral : 25.109 177.200 4154 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.95 % Allowed : 19.71 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.23), residues: 1308 helix: 2.06 (0.22), residues: 546 sheet: 1.70 (0.32), residues: 262 loop : -1.91 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 100 TYR 0.022 0.002 TYR A 650 PHE 0.023 0.002 PHE B 528 TRP 0.008 0.002 TRP A 567 HIS 0.005 0.001 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (14100) covalent geometry : angle 0.71887 / 0.38 (19704) SS BOND : bond 0.00242 / 0.12 ( 6) SS BOND : angle 0.74871 / 0.47 ( 12) hydrogen bonds : bond 0.06770 / 4.45 ( 658) hydrogen bonds : angle 4.61438 / 3.23 ( 1776) metal coordination : bond 0.00551 / 0.27 ( 6) link_BETA1-4 : bond 0.01102 / 0.56 ( 4) link_BETA1-4 : angle 4.34584 / 2.76 ( 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 189 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 0.456 Fit side-chains REVERT: A 221 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8515 (tp30) REVERT: A 246 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6169 (ptpp) REVERT: A 432 GLN cc_start: 0.7489 (mt0) cc_final: 0.7093 (tt0) REVERT: B 221 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8540 (tp30) REVERT: B 246 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6177 (ptpp) REVERT: B 432 GLN cc_start: 0.7492 (mt0) cc_final: 0.7095 (tt0) outliers start: 58 outliers final: 37 residues processed: 166 average time/residue: 0.4991 time to fit residues: 92.4443 Evaluate side-chains 164 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.182251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112680 restraints weight = 13955.094| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.24 r_work: 0.3266 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1097 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= 0.149 Angle : 0.648 9.223 19728 Z= 0.335 Chirality : 0.044 0.208 2410 Planarity : 0.005 0.067 1946 Dihedral : 23.542 172.342 4146 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.61 % Allowed : 19.28 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1308 helix: 2.22 (0.22), residues: 548 sheet: 1.81 (0.33), residues: 262 loop : -1.69 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 60 TYR 0.023 0.002 TYR A 650 PHE 0.015 0.001 PHE A 528 TRP 0.007 0.001 TRP A 567 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (14100) covalent geometry : angle 0.63902 / 0.33 (19704) SS BOND : bond 0.00086 / 0.04 ( 6) SS BOND : angle 0.43489 / 0.29 ( 12) hydrogen bonds : bond 0.05601 / 3.66 ( 658) hydrogen bonds : angle 4.44559 / 3.11 ( 1776) metal coordination : bond 0.00269 / 0.14 ( 6) link_BETA1-4 : bond 0.01372 / 0.69 ( 4) link_BETA1-4 : angle 4.50531 / 2.88 ( 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 188 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 134 time to evaluate : 0.436 Fit side-chains REVERT: A 246 LYS cc_start: 0.6313 (OUTLIER) cc_final: 0.6112 (pmtt) REVERT: A 272 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7862 (mtmm) REVERT: A 430 MET cc_start: 0.6706 (mtp) cc_final: 0.6501 (mtp) REVERT: B 246 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.6077 (pmtt) REVERT: B 272 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7860 (mtmm) REVERT: B 430 MET cc_start: 0.6696 (mtp) cc_final: 0.6491 (mtp) outliers start: 54 outliers final: 21 residues processed: 169 average time/residue: 0.5168 time to fit residues: 96.9153 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain 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 261 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 701 LEU 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: 3.9990 chunk 71 optimal weight: 40.0000 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN B 432 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 = 0.4207 r_free = 0.4207 target = 0.181323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112344 restraints weight = 13908.052| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.24 r_work: 0.3229 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14116 Z= 0.174 Angle : 0.660 8.939 19728 Z= 0.341 Chirality : 0.045 0.233 2410 Planarity : 0.005 0.070 1946 Dihedral : 22.784 168.818 4144 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.72 % Allowed : 18.34 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1308 helix: 2.21 (0.21), residues: 546 sheet: 1.68 (0.33), residues: 262 loop : -1.77 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.024 0.002 TYR B 650 PHE 0.020 0.002 PHE A 528 TRP 0.007 0.001 TRP A 567 HIS 0.005 0.001 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (14100) covalent geometry : angle 0.64918 / 0.34 (19704) SS BOND : bond 0.00169 / 0.08 ( 6) SS BOND : angle 0.60171 / 0.39 ( 12) hydrogen bonds : bond 0.05953 / 3.93 ( 658) hydrogen bonds : angle 4.42452 / 3.10 ( 1776) metal coordination : bond 0.00254 / 0.12 ( 6) link_BETA1-4 : bond 0.01327 / 0.67 ( 4) link_BETA1-4 : angle 4.94477 / 3.07 ( 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 199 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 132 time to evaluate : 0.485 Fit side-chains REVERT: A 246 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.6011 (pmtt) REVERT: A 430 MET cc_start: 0.6680 (mtp) cc_final: 0.6448 (mtp) REVERT: A 674 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7594 (mp) REVERT: B 246 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.6021 (pmtt) REVERT: B 430 MET cc_start: 0.6672 (mtp) cc_final: 0.6442 (mtp) REVERT: B 674 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7562 (mp) outliers start: 67 outliers final: 39 residues processed: 174 average time/residue: 0.4863 time to fit residues: 94.3061 Evaluate side-chains 176 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 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 246 LYS 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 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 684 HIS 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 129 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 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 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 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: 4.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 139 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN B 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.183125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117007 restraints weight = 13883.713| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.14 r_work: 0.3238 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1462 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= 0.131 Angle : 0.586 8.568 19728 Z= 0.311 Chirality : 0.043 0.226 2410 Planarity : 0.004 0.066 1946 Dihedral : 22.192 167.568 4143 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.86 % Allowed : 19.20 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.23), residues: 1308 helix: 2.40 (0.22), residues: 548 sheet: 1.86 (0.33), residues: 262 loop : -1.70 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.022 0.001 TYR B 650 PHE 0.026 0.001 PHE A 513 TRP 0.007 0.001 TRP B 567 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (14100) covalent geometry : angle 0.57347 / 0.31 (19704) SS BOND : bond 0.00047 / 0.02 ( 6) SS BOND : angle 0.27138 / 0.18 ( 12) hydrogen bonds : bond 0.05269 / 3.46 ( 658) hydrogen bonds : angle 4.32407 / 3.03 ( 1776) metal coordination : bond 0.00172 / 0.08 ( 6) link_BETA1-4 : bond 0.01576 / 0.80 ( 4) link_BETA1-4 : angle 5.01837 / 3.16 ( 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 188 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.460 Fit side-chains REVERT: A 272 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7738 (mtmm) REVERT: A 430 MET cc_start: 0.6792 (mtp) cc_final: 0.6539 (mtp) REVERT: A 457 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7731 (mmp) REVERT: A 659 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7561 (p0) REVERT: A 674 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7525 (mp) REVERT: B 272 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7742 (mtmm) REVERT: B 430 MET cc_start: 0.6775 (mtp) cc_final: 0.6524 (mtp) REVERT: B 457 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.7808 (mmp) REVERT: B 659 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7571 (p0) REVERT: B 674 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7530 (mp) outliers start: 57 outliers final: 28 residues processed: 160 average time/residue: 0.5333 time to fit residues: 94.5652 Evaluate side-chains 163 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.0270 chunk 70 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 450 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.182197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112816 restraints weight = 13870.929| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.29 r_work: 0.3250 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14116 Z= 0.159 Angle : 0.628 10.957 19728 Z= 0.330 Chirality : 0.043 0.228 2410 Planarity : 0.004 0.068 1946 Dihedral : 22.043 166.465 4134 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.61 % Allowed : 19.62 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1308 helix: 2.36 (0.21), residues: 546 sheet: 1.78 (0.32), residues: 262 loop : -1.78 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 570 TYR 0.023 0.002 TYR B 650 PHE 0.017 0.002 PHE A 528 TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (14100) covalent geometry : angle 0.61542 / 0.33 (19704) SS BOND : bond 0.00120 / 0.06 ( 6) SS BOND : angle 0.49941 / 0.32 ( 12) hydrogen bonds : bond 0.05620 / 3.71 ( 658) hydrogen bonds : angle 4.35551 / 3.05 ( 1776) metal coordination : bond 0.00304 / 0.15 ( 6) link_BETA1-4 : bond 0.01509 / 0.77 ( 4) link_BETA1-4 : angle 5.15239 / 3.20 ( 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 185 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 0.416 Fit side-chains REVERT: A 430 MET cc_start: 0.6783 (mtp) cc_final: 0.6533 (mtp) REVERT: A 659 ASN cc_start: 0.7932 (p0) cc_final: 0.7671 (p0) REVERT: A 674 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7713 (mp) REVERT: B 430 MET cc_start: 0.6771 (mtp) cc_final: 0.6521 (mtp) REVERT: B 659 ASN cc_start: 0.7943 (p0) cc_final: 0.7681 (p0) REVERT: B 674 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7719 (mp) outliers start: 54 outliers final: 33 residues processed: 161 average time/residue: 0.4777 time to fit residues: 85.8020 Evaluate side-chains 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 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 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain 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 261 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 0.2980 chunk 85 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 450 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.183693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113957 restraints weight = 13837.515| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.30 r_work: 0.3290 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14116 Z= 0.122 Angle : 0.565 8.357 19728 Z= 0.300 Chirality : 0.041 0.225 2410 Planarity : 0.004 0.066 1946 Dihedral : 21.764 166.417 4134 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.52 % Allowed : 19.88 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1308 helix: 2.52 (0.22), residues: 548 sheet: 1.92 (0.32), residues: 264 loop : -1.66 (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 0.013 0.001 PHE B 513 TRP 0.007 0.001 TRP B 567 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (14100) covalent geometry : angle 0.55139 / 0.30 (19704) SS BOND : bond 0.00042 / 0.02 ( 6) SS BOND : angle 0.23147 / 0.17 ( 12) hydrogen bonds : bond 0.05023 / 3.29 ( 658) hydrogen bonds : angle 4.24455 / 2.97 ( 1776) metal coordination : bond 0.00207 / 0.11 ( 6) link_BETA1-4 : bond 0.01627 / 0.82 ( 4) link_BETA1-4 : angle 5.04120 / 3.10 ( 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 186 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.456 Fit side-chains REVERT: A 272 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7799 (mtmm) REVERT: A 430 MET cc_start: 0.6781 (mtp) cc_final: 0.6527 (mtp) REVERT: A 457 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7838 (mmp) REVERT: A 674 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 272 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7801 (mtmm) REVERT: B 430 MET cc_start: 0.6781 (mtp) cc_final: 0.6526 (mtp) REVERT: B 457 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7725 (mmp) REVERT: B 659 ASN cc_start: 0.7899 (p0) cc_final: 0.7622 (p0) REVERT: B 674 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7628 (mp) outliers start: 53 outliers final: 29 residues processed: 165 average time/residue: 0.4175 time to fit residues: 77.2126 Evaluate side-chains 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 457 MET 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 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 729 LYS 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: 4.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 ASN B 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.180597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110936 restraints weight = 13570.494| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.22 r_work: 0.3232 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14116 Z= 0.238 Angle : 0.692 8.501 19728 Z= 0.360 Chirality : 0.046 0.232 2410 Planarity : 0.005 0.067 1946 Dihedral : 21.863 164.123 4134 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.18 % Allowed : 20.22 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.23), residues: 1308 helix: 2.09 (0.21), residues: 546 sheet: 1.59 (0.32), residues: 262 loop : -1.87 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 60 TYR 0.022 0.002 TYR B 650 PHE 0.024 0.002 PHE B 528 TRP 0.006 0.002 TRP A 567 HIS 0.007 0.001 HIS B 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (14100) covalent geometry : angle 0.67875 / 0.36 (19704) SS BOND : bond 0.00258 / 0.13 ( 6) SS BOND : angle 0.82247 / 0.51 ( 12) hydrogen bonds : bond 0.06573 / 4.36 ( 658) hydrogen bonds : angle 4.50289 / 3.16 ( 1776) metal coordination : bond 0.00612 / 0.29 ( 6) link_BETA1-4 : bond 0.01342 / 0.68 ( 4) link_BETA1-4 : angle 5.38206 / 3.33 ( 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 170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.468 Fit side-chains REVERT: A 430 MET cc_start: 0.6832 (mtp) cc_final: 0.6567 (mtp) REVERT: A 674 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7668 (mp) REVERT: B 430 MET cc_start: 0.6832 (mtp) cc_final: 0.6567 (mtp) REVERT: B 674 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7666 (mp) outliers start: 49 outliers final: 36 residues processed: 154 average time/residue: 0.4612 time to fit residues: 79.7162 Evaluate side-chains 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 636 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 727 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 261 ILE Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 636 ILE 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 727 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: 5.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.182744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113035 restraints weight = 13725.574| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.29 r_work: 0.3253 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14116 Z= 0.135 Angle : 0.585 8.354 19728 Z= 0.310 Chirality : 0.042 0.240 2410 Planarity : 0.004 0.065 1946 Dihedral : 21.683 163.783 4134 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.75 % Allowed : 20.73 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.23), residues: 1308 helix: 2.37 (0.21), residues: 546 sheet: 1.73 (0.32), residues: 262 loop : -1.79 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.022 0.001 TYR A 650 PHE 0.014 0.001 PHE B 528 TRP 0.006 0.001 TRP A 567 HIS 0.003 0.001 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (14100) covalent geometry : angle 0.57216 / 0.31 (19704) SS BOND : bond 0.00040 / 0.02 ( 6) SS BOND : angle 0.30936 / 0.21 ( 12) hydrogen bonds : bond 0.05467 / 3.59 ( 658) hydrogen bonds : angle 4.34946 / 3.05 ( 1776) metal coordination : bond 0.00228 / 0.12 ( 6) link_BETA1-4 : bond 0.01536 / 0.78 ( 4) link_BETA1-4 : angle 5.02243 / 3.11 ( 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 170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.452 Fit side-chains REVERT: A 272 LYS cc_start: 0.8329 (mtpp) cc_final: 0.7858 (mtmm) REVERT: A 430 MET cc_start: 0.6823 (mtp) cc_final: 0.6551 (mtp) REVERT: A 457 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7881 (mmp) REVERT: A 659 ASN cc_start: 0.7894 (p0) cc_final: 0.7679 (p0) REVERT: A 674 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7651 (mp) REVERT: B 272 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7854 (mtmm) REVERT: B 430 MET cc_start: 0.6817 (mtp) cc_final: 0.6549 (mtp) REVERT: B 674 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7654 (mp) outliers start: 44 outliers final: 27 residues processed: 153 average time/residue: 0.4501 time to fit residues: 76.4752 Evaluate side-chains 157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 457 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 40.0000 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.183355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114022 restraints weight = 13632.392| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.26 r_work: 0.3255 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14116 Z= 0.141 Angle : 0.578 8.346 19728 Z= 0.305 Chirality : 0.042 0.246 2410 Planarity : 0.004 0.065 1946 Dihedral : 21.419 163.789 4134 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.65 % Allowed : 21.93 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.23), residues: 1308 helix: 2.44 (0.21), residues: 548 sheet: 1.77 (0.32), residues: 262 loop : -1.70 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 100 TYR 0.023 0.002 TYR B 650 PHE 0.018 0.002 PHE A 513 TRP 0.008 0.001 TRP B 567 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14100) covalent geometry : angle 0.56520 / 0.30 (19704) SS BOND : bond 0.00141 / 0.07 ( 6) SS BOND : angle 0.53454 / 0.32 ( 12) hydrogen bonds : bond 0.05262 / 3.44 ( 658) hydrogen bonds : angle 4.28422 / 3.01 ( 1776) metal coordination : bond 0.00297 / 0.14 ( 6) link_BETA1-4 : bond 0.01421 / 0.72 ( 4) link_BETA1-4 : angle 4.98492 / 3.11 ( 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 163 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.458 Fit side-chains REVERT: A 272 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7815 (mtmm) REVERT: A 307 LYS cc_start: 0.8194 (mttp) cc_final: 0.7983 (mtmt) REVERT: A 430 MET cc_start: 0.6754 (mtp) cc_final: 0.6492 (mtp) REVERT: A 457 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.7842 (mmp) REVERT: A 659 ASN cc_start: 0.7870 (p0) cc_final: 0.7640 (p0) REVERT: B 272 LYS cc_start: 0.8285 (mtpp) cc_final: 0.7778 (mtmm) REVERT: B 307 LYS cc_start: 0.8188 (mttp) cc_final: 0.7979 (mtmt) REVERT: B 430 MET cc_start: 0.6765 (mtp) cc_final: 0.6501 (mtp) REVERT: B 659 ASN cc_start: 0.7851 (p0) cc_final: 0.7633 (p0) outliers start: 31 outliers final: 25 residues processed: 152 average time/residue: 0.4566 time to fit residues: 77.6157 Evaluate side-chains 153 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 457 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 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 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.182095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113036 restraints weight = 13568.662| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.34 r_work: 0.3221 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14116 Z= 0.170 Angle : 0.612 8.367 19728 Z= 0.320 Chirality : 0.043 0.257 2410 Planarity : 0.004 0.065 1946 Dihedral : 21.426 164.017 4130 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.90 % Allowed : 21.59 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1308 helix: 2.30 (0.21), residues: 546 sheet: 1.61 (0.33), residues: 262 loop : -1.78 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 570 TYR 0.021 0.002 TYR B 650 PHE 0.019 0.002 PHE A 528 TRP 0.006 0.001 TRP A 567 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (14100) covalent geometry : angle 0.59972 / 0.32 (19704) SS BOND : bond 0.00172 / 0.09 ( 6) SS BOND : angle 0.40229 / 0.27 ( 12) hydrogen bonds : bond 0.05833 / 3.84 ( 658) hydrogen bonds : angle 4.40157 / 3.09 ( 1776) metal coordination : bond 0.00366 / 0.18 ( 6) link_BETA1-4 : bond 0.01335 / 0.68 ( 4) link_BETA1-4 : angle 5.02377 / 3.13 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7398.58 seconds wall clock time: 126 minutes 20.70 seconds (7580.70 seconds total)