Starting phenix.real_space_refine on Sat Jul 4 00:53:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cz9_46064/07_2026/9cz9_46064.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cz9_46064/07_2026/9cz9_46064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cz9_46064/07_2026/9cz9_46064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cz9_46064/07_2026/9cz9_46064.map" model { file = "/net/cci-nas-00/data/ceres_data/9cz9_46064/07_2026/9cz9_46064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cz9_46064/07_2026/9cz9_46064.cif" } resolution = 2.43 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= 1.000 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: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 48 5.16 5 C 10656 2.51 5 N 2688 2.21 5 O 3696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 17112 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1379 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1397 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 1.79, per 1000 atoms: 0.10 Number of scatterers: 17112 At special positions: 0 Unit cell: (106.95, 112.47, 104.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 48 16.00 O 3696 8.00 N 2688 7.00 C 10656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG BCYS A 94 " distance=2.05 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG BCYS B 94 " distance=2.05 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG BCYS C 94 " distance=2.05 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG BCYS D 94 " distance=2.05 Simple disulfide: pdb=" SG CYS E 118 " - pdb=" SG BCYS E 94 " distance=2.05 Simple disulfide: pdb=" SG CYS F 118 " - pdb=" SG BCYS F 94 " distance=2.05 Simple disulfide: pdb=" SG CYS G 118 " - pdb=" SG BCYS G 94 " distance=2.05 Simple disulfide: pdb=" SG CYS H 118 " - pdb=" SG BCYS H 94 " distance=2.05 Simple disulfide: pdb=" SG CYS I 118 " - pdb=" SG BCYS I 94 " distance=2.05 Simple disulfide: pdb=" SG CYS J 118 " - pdb=" SG BCYS J 94 " distance=2.05 Simple disulfide: pdb=" SG CYS K 118 " - pdb=" SG BCYS K 94 " distance=2.05 Simple disulfide: pdb=" SG CYS L 118 " - pdb=" SG BCYS L 94 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 984.2 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 15 through 44 removed outlier: 3.653A pdb=" N THR A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 104 through 128 Processing helix chain 'A' and resid 134 through 161 removed outlier: 3.667A pdb=" N GLU A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'B' and resid 15 through 44 removed outlier: 3.653A pdb=" N THR B 38 " --> pdb=" O TYR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 104 through 128 Processing helix chain 'B' and resid 134 through 161 removed outlier: 3.667A pdb=" N GLU B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'C' and resid 15 through 44 removed outlier: 3.653A pdb=" N THR C 38 " --> pdb=" O TYR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 77 removed outlier: 3.941A pdb=" N ALA C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 72 - end of helix Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 104 through 128 Processing helix chain 'C' and resid 134 through 161 removed outlier: 3.666A pdb=" N GLU C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'D' and resid 15 through 44 removed outlier: 3.653A pdb=" N THR D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 77 removed outlier: 3.941A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 128 Processing helix chain 'D' and resid 134 through 161 removed outlier: 3.666A pdb=" N GLU D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'E' and resid 15 through 44 removed outlier: 3.653A pdb=" N THR E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 104 through 128 Processing helix chain 'E' and resid 134 through 161 removed outlier: 3.667A pdb=" N GLU E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 15 through 44 removed outlier: 3.652A pdb=" N THR F 38 " --> pdb=" O TYR F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 104 through 128 Processing helix chain 'F' and resid 134 through 161 removed outlier: 3.667A pdb=" N GLU F 147 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'G' and resid 15 through 44 removed outlier: 3.652A pdb=" N THR G 38 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 72 - end of helix Processing helix chain 'G' and resid 84 through 90 Processing helix chain 'G' and resid 104 through 128 Processing helix chain 'G' and resid 134 through 161 removed outlier: 3.666A pdb=" N GLU G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'H' and resid 15 through 44 removed outlier: 3.652A pdb=" N THR H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 72 - end of helix Processing helix chain 'H' and resid 84 through 90 Processing helix chain 'H' and resid 104 through 128 Processing helix chain 'H' and resid 134 through 161 removed outlier: 3.667A pdb=" N GLU H 147 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 182 Processing helix chain 'I' and resid 15 through 44 removed outlier: 3.653A pdb=" N THR I 38 " --> pdb=" O TYR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.941A pdb=" N ALA I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 72 - end of helix Processing helix chain 'I' and resid 84 through 90 Processing helix chain 'I' and resid 104 through 128 Processing helix chain 'I' and resid 134 through 161 removed outlier: 3.667A pdb=" N GLU I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 182 Processing helix chain 'J' and resid 15 through 44 removed outlier: 3.653A pdb=" N THR J 38 " --> pdb=" O TYR J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 72 - end of helix Processing helix chain 'J' and resid 84 through 90 Processing helix chain 'J' and resid 104 through 128 Processing helix chain 'J' and resid 134 through 161 removed outlier: 3.667A pdb=" N GLU J 147 " --> pdb=" O ALA J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'K' and resid 15 through 44 removed outlier: 3.652A pdb=" N THR K 38 " --> pdb=" O TYR K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 72 - end of helix Processing helix chain 'K' and resid 84 through 90 Processing helix chain 'K' and resid 104 through 128 Processing helix chain 'K' and resid 134 through 161 removed outlier: 3.667A pdb=" N GLU K 147 " --> pdb=" O ALA K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 182 Processing helix chain 'L' and resid 15 through 44 removed outlier: 3.653A pdb=" N THR L 38 " --> pdb=" O TYR L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 77 removed outlier: 3.940A pdb=" N ALA L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) Proline residue: L 72 - end of helix Processing helix chain 'L' and resid 84 through 90 Processing helix chain 'L' and resid 104 through 128 Processing helix chain 'L' and resid 134 through 161 removed outlier: 3.668A pdb=" N GLU L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 182 1152 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5495 1.35 - 1.48: 4121 1.48 - 1.61: 7280 1.61 - 1.74: 0 1.74 - 1.86: 60 Bond restraints: 16956 Sorted by residual: bond pdb=" CG ARG G 169 " pdb=" CD ARG G 169 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" CG ARG F 169 " pdb=" CD ARG F 169 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.43e+00 bond pdb=" CG ARG H 169 " pdb=" CD ARG H 169 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" CG ARG K 169 " pdb=" CD ARG K 169 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.38e+00 bond pdb=" CG ARG A 169 " pdb=" CD ARG A 169 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.37e+00 ... (remaining 16951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 21548 1.68 - 3.36: 1252 3.36 - 5.04: 132 5.04 - 6.72: 36 6.72 - 8.40: 48 Bond angle restraints: 23016 Sorted by residual: angle pdb=" C GLY D 165 " pdb=" N HIS D 166 " pdb=" CA HIS D 166 " ideal model delta sigma weight residual 122.92 115.90 7.02 1.76e+00 3.23e-01 1.59e+01 angle pdb=" C GLY L 165 " pdb=" N HIS L 166 " pdb=" CA HIS L 166 " ideal model delta sigma weight residual 122.92 115.91 7.01 1.76e+00 3.23e-01 1.59e+01 angle pdb=" C GLY C 165 " pdb=" N HIS C 166 " pdb=" CA HIS C 166 " ideal model delta sigma weight residual 122.92 115.92 7.00 1.76e+00 3.23e-01 1.58e+01 angle pdb=" C GLY H 165 " pdb=" N HIS H 166 " pdb=" CA HIS H 166 " ideal model delta sigma weight residual 122.92 115.94 6.98 1.76e+00 3.23e-01 1.58e+01 angle pdb=" C GLY J 165 " pdb=" N HIS J 166 " pdb=" CA HIS J 166 " ideal model delta sigma weight residual 122.92 115.94 6.98 1.76e+00 3.23e-01 1.57e+01 ... (remaining 23011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 9371 17.17 - 34.34: 769 34.34 - 51.51: 84 51.51 - 68.68: 36 68.68 - 85.84: 36 Dihedral angle restraints: 10296 sinusoidal: 4212 harmonic: 6084 Sorted by residual: dihedral pdb=" CA GLU H 80 " pdb=" C GLU H 80 " pdb=" N LEU H 81 " pdb=" CA LEU H 81 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA GLU K 80 " pdb=" C GLU K 80 " pdb=" N LEU K 81 " pdb=" CA LEU K 81 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA GLU J 80 " pdb=" C GLU J 80 " pdb=" N LEU J 81 " pdb=" CA LEU J 81 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 10293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1460 0.037 - 0.074: 700 0.074 - 0.111: 273 0.111 - 0.148: 73 0.148 - 0.185: 26 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CG LEU K 70 " pdb=" CB LEU K 70 " pdb=" CD1 LEU K 70 " pdb=" CD2 LEU K 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CG LEU D 70 " pdb=" CB LEU D 70 " pdb=" CD1 LEU D 70 " pdb=" CD2 LEU D 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CG LEU L 70 " pdb=" CB LEU L 70 " pdb=" CD1 LEU L 70 " pdb=" CD2 LEU L 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 2529 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS H 166 " -0.037 2.00e-02 2.50e+03 3.25e-02 1.58e+01 pdb=" CG HIS H 166 " 0.068 2.00e-02 2.50e+03 pdb=" ND1 HIS H 166 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS H 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS H 166 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS H 166 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 166 " -0.037 2.00e-02 2.50e+03 3.24e-02 1.58e+01 pdb=" CG HIS D 166 " 0.068 2.00e-02 2.50e+03 pdb=" ND1 HIS D 166 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS D 166 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS D 166 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 166 " -0.037 2.00e-02 2.50e+03 3.24e-02 1.58e+01 pdb=" CG HIS G 166 " 0.068 2.00e-02 2.50e+03 pdb=" ND1 HIS G 166 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS G 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS G 166 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS G 166 " -0.009 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 395 2.53 - 3.12: 13289 3.12 - 3.71: 30574 3.71 - 4.31: 44922 4.31 - 4.90: 70080 Nonbonded interactions: 159260 Sorted by model distance: nonbonded pdb=" OE1 GLU L 30 " pdb="FE FE L 201 " model vdw 1.937 3.000 nonbonded pdb=" OE1 GLU C 30 " pdb="FE FE C 201 " model vdw 1.937 3.000 nonbonded pdb=" OE1 GLU K 30 " pdb="FE FE K 201 " model vdw 1.937 3.000 nonbonded pdb=" OE1 GLU I 30 " pdb="FE FE I 201 " model vdw 1.937 3.000 nonbonded pdb=" OE1 GLU G 30 " pdb="FE FE G 201 " model vdw 1.938 3.000 ... (remaining 159255 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.390 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.006 0.056 16968 Z= 0.250 Angle : 0.948 8.398 23040 Z= 0.509 Chirality : 0.052 0.185 2532 Planarity : 0.009 0.050 2988 Dihedral : 13.778 85.844 6372 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.16), residues: 2040 helix: -1.75 (0.11), residues: 1440 sheet: None (None), residues: 0 loop : -0.13 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.004 ARG E 73 TYR 0.026 0.008 TYR I 98 PHE 0.032 0.009 PHE I 181 TRP 0.016 0.006 TRP I 154 HIS 0.026 0.007 HIS K 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (16956) covalent geometry : angle 0.94098 / 0.51 (23016) SS BOND : bond 0.01989 / 1.20 ( 12) SS BOND : angle 3.73035 / 2.15 ( 24) hydrogen bonds : bond 0.18610 / 12.51 ( 1152) hydrogen bonds : angle 8.27807 / 5.70 ( 3372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.677 Fit side-chains REVERT: A 171 LYS cc_start: 0.6478 (tttt) cc_final: 0.5725 (ttpt) REVERT: B 171 LYS cc_start: 0.6553 (tttt) cc_final: 0.5752 (ttpt) REVERT: C 171 LYS cc_start: 0.6622 (tttt) cc_final: 0.5834 (ttpt) REVERT: D 171 LYS cc_start: 0.6453 (tttt) cc_final: 0.5593 (ttpt) REVERT: E 171 LYS cc_start: 0.6442 (tttt) cc_final: 0.5742 (ttpt) REVERT: F 171 LYS cc_start: 0.6501 (tttt) cc_final: 0.5525 (tmtt) REVERT: G 171 LYS cc_start: 0.6523 (tttt) cc_final: 0.5745 (ttpt) REVERT: H 171 LYS cc_start: 0.6430 (tttt) cc_final: 0.5682 (ttpt) REVERT: I 171 LYS cc_start: 0.6521 (tttt) cc_final: 0.5406 (pptt) REVERT: J 171 LYS cc_start: 0.6496 (tttt) cc_final: 0.5479 (tmtt) REVERT: K 171 LYS cc_start: 0.6429 (tttt) cc_final: 0.5693 (ttpt) REVERT: L 171 LYS cc_start: 0.6529 (tttt) cc_final: 0.5719 (ttpt) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.6423 time to fit residues: 211.3757 Evaluate side-chains 244 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 ASN ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.187564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175302 restraints weight = 46255.705| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.25 r_work: 0.3896 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16968 Z= 0.177 Angle : 0.589 4.468 23040 Z= 0.332 Chirality : 0.038 0.126 2532 Planarity : 0.005 0.031 2988 Dihedral : 4.492 19.143 2316 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.21 % Allowed : 6.95 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.18), residues: 2040 helix: 0.75 (0.12), residues: 1416 sheet: None (None), residues: 0 loop : 0.66 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 95 TYR 0.019 0.002 TYR E 123 PHE 0.031 0.003 PHE A 31 TRP 0.008 0.002 TRP L 154 HIS 0.005 0.002 HIS F 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (16956) covalent geometry : angle 0.58809 / 0.33 (23016) SS BOND : bond 0.00413 / 0.25 ( 12) SS BOND : angle 1.12175 / 0.70 ( 24) hydrogen bonds : bond 0.07551 / 5.04 ( 1152) hydrogen bonds : angle 5.81690 / 4.00 ( 3372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.452 Fit side-chains REVERT: A 171 LYS cc_start: 0.6458 (tttt) cc_final: 0.5618 (ttpt) REVERT: B 171 LYS cc_start: 0.6395 (tttt) cc_final: 0.5442 (ttpt) REVERT: C 171 LYS cc_start: 0.6471 (tttt) cc_final: 0.5590 (ttpt) REVERT: C 179 SER cc_start: 0.8797 (m) cc_final: 0.8540 (p) REVERT: D 171 LYS cc_start: 0.6262 (tttt) cc_final: 0.5470 (ttpt) REVERT: E 171 LYS cc_start: 0.6320 (tttt) cc_final: 0.5485 (ttpt) REVERT: E 179 SER cc_start: 0.8845 (m) cc_final: 0.8553 (p) REVERT: F 171 LYS cc_start: 0.6473 (tttt) cc_final: 0.5632 (ttpt) REVERT: G 171 LYS cc_start: 0.6113 (tttt) cc_final: 0.4961 (tmtt) REVERT: H 171 LYS cc_start: 0.6164 (tttt) cc_final: 0.5329 (ttpt) REVERT: H 179 SER cc_start: 0.8800 (m) cc_final: 0.8531 (p) REVERT: I 116 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8472 (mm-30) REVERT: I 171 LYS cc_start: 0.6360 (tttt) cc_final: 0.5212 (pptt) REVERT: J 171 LYS cc_start: 0.6309 (tttt) cc_final: 0.5234 (tmtt) REVERT: K 171 LYS cc_start: 0.6360 (tttt) cc_final: 0.5572 (ttpt) REVERT: L 171 LYS cc_start: 0.6295 (tttt) cc_final: 0.5353 (ttpt) outliers start: 21 outliers final: 9 residues processed: 268 average time/residue: 0.6662 time to fit residues: 195.4959 Evaluate side-chains 240 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 231 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain K residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 152 optimal weight: 0.0040 chunk 126 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 202 optimal weight: 0.0270 chunk 43 optimal weight: 0.4980 chunk 107 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 overall best weight: 0.2850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.192518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.180855 restraints weight = 45832.820| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.17 r_work: 0.3966 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16968 Z= 0.139 Angle : 0.522 5.962 23040 Z= 0.292 Chirality : 0.037 0.124 2532 Planarity : 0.004 0.038 2988 Dihedral : 4.212 22.328 2316 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 8.51 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.18), residues: 2040 helix: 1.57 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 0.93 (0.29), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 95 TYR 0.016 0.001 TYR D 75 PHE 0.029 0.002 PHE B 31 TRP 0.014 0.002 TRP C 154 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (16956) covalent geometry : angle 0.52152 / 0.29 (23016) SS BOND : bond 0.00404 / 0.24 ( 12) SS BOND : angle 0.92357 / 0.58 ( 24) hydrogen bonds : bond 0.06374 / 4.26 ( 1152) hydrogen bonds : angle 5.41930 / 3.73 ( 3372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 266 time to evaluate : 0.488 Fit side-chains REVERT: A 171 LYS cc_start: 0.6452 (tttt) cc_final: 0.5678 (ttpt) REVERT: A 179 SER cc_start: 0.8788 (m) cc_final: 0.8521 (p) REVERT: B 116 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7955 (mp0) REVERT: B 171 LYS cc_start: 0.6463 (tttt) cc_final: 0.5648 (ttpt) REVERT: C 171 LYS cc_start: 0.6484 (tttt) cc_final: 0.5716 (ttpt) REVERT: C 179 SER cc_start: 0.8728 (m) cc_final: 0.8469 (p) REVERT: D 171 LYS cc_start: 0.6334 (tttt) cc_final: 0.5643 (ttpt) REVERT: E 171 LYS cc_start: 0.6385 (tttt) cc_final: 0.5633 (ttpt) REVERT: E 179 SER cc_start: 0.8798 (m) cc_final: 0.8517 (p) REVERT: F 171 LYS cc_start: 0.6504 (tttt) cc_final: 0.5599 (pptt) REVERT: G 171 LYS cc_start: 0.6142 (tttt) cc_final: 0.5365 (ttpt) REVERT: H 171 LYS cc_start: 0.6294 (tttt) cc_final: 0.5557 (ttpt) REVERT: H 179 SER cc_start: 0.8744 (m) cc_final: 0.8503 (p) REVERT: I 171 LYS cc_start: 0.6469 (tttt) cc_final: 0.5483 (pptt) REVERT: J 171 LYS cc_start: 0.6436 (tttt) cc_final: 0.5678 (ttpt) REVERT: K 171 LYS cc_start: 0.6443 (tttt) cc_final: 0.5765 (ttpt) REVERT: K 179 SER cc_start: 0.8819 (m) cc_final: 0.8561 (p) REVERT: L 125 GLU cc_start: 0.8216 (tt0) cc_final: 0.7998 (tt0) REVERT: L 171 LYS cc_start: 0.6421 (tttt) cc_final: 0.5651 (ttpt) outliers start: 8 outliers final: 3 residues processed: 268 average time/residue: 0.6929 time to fit residues: 202.8751 Evaluate side-chains 235 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 14 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 25 optimal weight: 0.0020 chunk 114 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS ** E 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.183503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.170508 restraints weight = 49470.527| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.38 r_work: 0.3817 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16968 Z= 0.189 Angle : 0.613 5.102 23040 Z= 0.340 Chirality : 0.040 0.142 2532 Planarity : 0.005 0.044 2988 Dihedral : 4.460 20.447 2316 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.67 % Allowed : 9.60 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.18), residues: 2040 helix: 1.53 (0.12), residues: 1416 sheet: None (None), residues: 0 loop : 1.05 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 95 TYR 0.020 0.003 TYR A 123 PHE 0.018 0.002 PHE F 31 TRP 0.017 0.002 TRP C 154 HIS 0.007 0.003 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (16956) covalent geometry : angle 0.61205 / 0.34 (23016) SS BOND : bond 0.00622 / 0.38 ( 12) SS BOND : angle 0.95032 / 0.60 ( 24) hydrogen bonds : bond 0.07615 / 5.10 ( 1152) hydrogen bonds : angle 5.53322 / 3.81 ( 3372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.728 Fit side-chains REVERT: A 171 LYS cc_start: 0.6198 (tttt) cc_final: 0.5296 (ttpt) REVERT: A 179 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 171 LYS cc_start: 0.6293 (tttt) cc_final: 0.5360 (ttpt) REVERT: C 162 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7397 (pptt) REVERT: C 171 LYS cc_start: 0.6456 (tttt) cc_final: 0.5534 (ttpt) REVERT: C 179 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8496 (p) REVERT: D 171 LYS cc_start: 0.6271 (tttt) cc_final: 0.5444 (ttpt) REVERT: E 171 LYS cc_start: 0.6162 (tttt) cc_final: 0.5067 (pptt) REVERT: F 171 LYS cc_start: 0.6345 (tttt) cc_final: 0.5477 (ttpt) REVERT: G 171 LYS cc_start: 0.5966 (tttt) cc_final: 0.5075 (ttpt) REVERT: H 125 GLU cc_start: 0.8398 (tt0) cc_final: 0.8156 (tt0) REVERT: H 171 LYS cc_start: 0.6094 (tttt) cc_final: 0.5282 (ttpt) REVERT: H 179 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8515 (p) REVERT: I 171 LYS cc_start: 0.6252 (tttt) cc_final: 0.5044 (pptt) REVERT: J 171 LYS cc_start: 0.6307 (tttt) cc_final: 0.5456 (ttpt) REVERT: K 41 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8378 (tmm-80) REVERT: K 171 LYS cc_start: 0.6240 (tttt) cc_final: 0.5435 (ttpt) REVERT: L 171 LYS cc_start: 0.6168 (tttt) cc_final: 0.5210 (ttpt) outliers start: 29 outliers final: 17 residues processed: 260 average time/residue: 0.7647 time to fit residues: 216.4798 Evaluate side-chains 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 41 ARG Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.0270 chunk 186 optimal weight: 0.0170 chunk 56 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.187818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.175720 restraints weight = 48951.840| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.20 r_work: 0.3895 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16968 Z= 0.143 Angle : 0.532 5.532 23040 Z= 0.299 Chirality : 0.037 0.130 2532 Planarity : 0.004 0.044 2988 Dihedral : 4.183 20.455 2316 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.72 % Allowed : 9.89 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.18), residues: 2040 helix: 1.88 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 1.16 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 95 TYR 0.020 0.002 TYR L 123 PHE 0.024 0.002 PHE I 31 TRP 0.020 0.002 TRP C 154 HIS 0.003 0.001 HIS H 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (16956) covalent geometry : angle 0.53182 / 0.30 (23016) SS BOND : bond 0.00516 / 0.31 ( 12) SS BOND : angle 0.95326 / 0.60 ( 24) hydrogen bonds : bond 0.06610 / 4.43 ( 1152) hydrogen bonds : angle 5.33493 / 3.67 ( 3372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 272 time to evaluate : 0.606 Fit side-chains REVERT: A 171 LYS cc_start: 0.6208 (tttt) cc_final: 0.5361 (ttpt) REVERT: A 179 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8537 (p) REVERT: B 171 LYS cc_start: 0.6241 (tttt) cc_final: 0.5343 (ttpt) REVERT: C 162 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7309 (pptt) REVERT: C 171 LYS cc_start: 0.6414 (tttt) cc_final: 0.5512 (ttpt) REVERT: C 179 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8517 (p) REVERT: D 171 LYS cc_start: 0.6192 (tttt) cc_final: 0.5390 (ttpt) REVERT: E 171 LYS cc_start: 0.6175 (tttt) cc_final: 0.5345 (ttpt) REVERT: F 171 LYS cc_start: 0.6280 (tttt) cc_final: 0.5235 (pptt) REVERT: F 179 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8488 (p) REVERT: G 171 LYS cc_start: 0.5967 (tttt) cc_final: 0.5109 (ttpt) REVERT: H 125 GLU cc_start: 0.8326 (tt0) cc_final: 0.8099 (tt0) REVERT: H 171 LYS cc_start: 0.6147 (tttt) cc_final: 0.5349 (ttpt) REVERT: H 179 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8490 (p) REVERT: I 171 LYS cc_start: 0.6289 (tttt) cc_final: 0.5324 (ttpt) REVERT: J 171 LYS cc_start: 0.6233 (tttt) cc_final: 0.5414 (ttpt) REVERT: K 41 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8320 (tmm-80) REVERT: K 54 GLU cc_start: 0.8110 (pm20) cc_final: 0.7794 (pm20) REVERT: K 171 LYS cc_start: 0.6263 (tttt) cc_final: 0.5477 (ttpt) REVERT: L 171 LYS cc_start: 0.6015 (tttt) cc_final: 0.5161 (ttpt) outliers start: 30 outliers final: 18 residues processed: 279 average time/residue: 0.7593 time to fit residues: 230.6419 Evaluate side-chains 268 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 41 ARG Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 176 optimal weight: 0.0040 chunk 3 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 96 optimal weight: 0.0050 chunk 137 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4806 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.187618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174094 restraints weight = 48976.972| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.40 r_work: 0.3868 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16968 Z= 0.137 Angle : 0.529 5.098 23040 Z= 0.295 Chirality : 0.036 0.130 2532 Planarity : 0.004 0.043 2988 Dihedral : 3.991 14.246 2316 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 1.61 % Allowed : 11.03 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.18), residues: 2040 helix: 1.96 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.42 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 95 TYR 0.020 0.002 TYR G 123 PHE 0.024 0.002 PHE B 31 TRP 0.021 0.003 TRP C 154 HIS 0.003 0.001 HIS K 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (16956) covalent geometry : angle 0.52827 / 0.30 (23016) SS BOND : bond 0.00498 / 0.30 ( 12) SS BOND : angle 0.96143 / 0.61 ( 24) hydrogen bonds : bond 0.06274 / 4.21 ( 1152) hydrogen bonds : angle 5.23244 / 3.60 ( 3372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.666 Fit side-chains REVERT: A 171 LYS cc_start: 0.6088 (tttt) cc_final: 0.5179 (ttpt) REVERT: A 179 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8446 (p) REVERT: B 171 LYS cc_start: 0.5927 (tttt) cc_final: 0.5016 (ttpt) REVERT: C 162 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7316 (pptt) REVERT: C 171 LYS cc_start: 0.6220 (tttt) cc_final: 0.5302 (ttpt) REVERT: C 179 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8462 (p) REVERT: D 171 LYS cc_start: 0.6000 (tttt) cc_final: 0.5153 (ttpt) REVERT: E 171 LYS cc_start: 0.6071 (tttt) cc_final: 0.5211 (ttpt) REVERT: F 171 LYS cc_start: 0.6178 (tttt) cc_final: 0.5276 (ttpt) REVERT: G 171 LYS cc_start: 0.5768 (tttt) cc_final: 0.4831 (ttpt) REVERT: H 125 GLU cc_start: 0.8279 (tt0) cc_final: 0.8069 (tt0) REVERT: H 171 LYS cc_start: 0.5922 (tttt) cc_final: 0.5110 (ttpt) REVERT: H 179 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8426 (p) REVERT: I 171 LYS cc_start: 0.6117 (tttt) cc_final: 0.4869 (pptt) REVERT: J 171 LYS cc_start: 0.6055 (tttt) cc_final: 0.5189 (ttpt) REVERT: K 54 GLU cc_start: 0.8023 (pm20) cc_final: 0.7706 (pm20) REVERT: K 171 LYS cc_start: 0.6085 (tttt) cc_final: 0.5261 (ttpt) REVERT: L 171 LYS cc_start: 0.5864 (tttt) cc_final: 0.4965 (ttpt) outliers start: 28 outliers final: 20 residues processed: 259 average time/residue: 0.7378 time to fit residues: 207.9706 Evaluate side-chains 259 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 202 optimal weight: 0.0570 chunk 50 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 163 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.186756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173183 restraints weight = 51342.186| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.34 r_work: 0.3837 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16968 Z= 0.140 Angle : 0.531 4.576 23040 Z= 0.296 Chirality : 0.036 0.132 2532 Planarity : 0.004 0.043 2988 Dihedral : 3.968 13.856 2316 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 1.78 % Allowed : 11.26 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.18), residues: 2040 helix: 2.07 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 1.38 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 95 TYR 0.017 0.002 TYR L 123 PHE 0.021 0.002 PHE K 31 TRP 0.017 0.003 TRP J 154 HIS 0.004 0.001 HIS H 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (16956) covalent geometry : angle 0.52984 / 0.30 (23016) SS BOND : bond 0.00558 / 0.34 ( 12) SS BOND : angle 1.00746 / 0.64 ( 24) hydrogen bonds : bond 0.06381 / 4.28 ( 1152) hydrogen bonds : angle 5.20484 / 3.58 ( 3372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.658 Fit side-chains REVERT: A 171 LYS cc_start: 0.6107 (tttt) cc_final: 0.5177 (ttpt) REVERT: A 179 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8448 (p) REVERT: B 171 LYS cc_start: 0.5900 (tttt) cc_final: 0.4979 (ttpt) REVERT: C 162 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7430 (pptt) REVERT: C 171 LYS cc_start: 0.6211 (tttt) cc_final: 0.5294 (ttpt) REVERT: C 179 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8480 (p) REVERT: D 171 LYS cc_start: 0.6090 (tttt) cc_final: 0.5208 (ttpt) REVERT: E 171 LYS cc_start: 0.6135 (tttt) cc_final: 0.5279 (ttpt) REVERT: F 171 LYS cc_start: 0.6286 (tttt) cc_final: 0.5157 (pptt) REVERT: G 171 LYS cc_start: 0.5813 (tttt) cc_final: 0.4885 (ttpt) REVERT: H 125 GLU cc_start: 0.8344 (tt0) cc_final: 0.8130 (tt0) REVERT: H 171 LYS cc_start: 0.5893 (tttt) cc_final: 0.5114 (ttpt) REVERT: H 179 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8406 (p) REVERT: I 171 LYS cc_start: 0.6033 (tttt) cc_final: 0.4654 (pptt) REVERT: J 171 LYS cc_start: 0.6084 (tttt) cc_final: 0.5233 (ttpt) REVERT: K 54 GLU cc_start: 0.8185 (pm20) cc_final: 0.7842 (pm20) REVERT: K 171 LYS cc_start: 0.6031 (tttt) cc_final: 0.5197 (ttpt) REVERT: L 171 LYS cc_start: 0.5874 (tttt) cc_final: 0.4977 (ttpt) outliers start: 31 outliers final: 24 residues processed: 261 average time/residue: 0.7069 time to fit residues: 200.7953 Evaluate side-chains 262 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 190 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.182438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.169134 restraints weight = 52909.497| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.34 r_work: 0.3794 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16968 Z= 0.192 Angle : 0.618 4.671 23040 Z= 0.344 Chirality : 0.039 0.145 2532 Planarity : 0.005 0.042 2988 Dihedral : 4.281 15.646 2316 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 1.95 % Allowed : 11.67 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.18), residues: 2040 helix: 1.70 (0.12), residues: 1416 sheet: None (None), residues: 0 loop : 1.36 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 95 TYR 0.022 0.003 TYR E 123 PHE 0.013 0.002 PHE B 31 TRP 0.017 0.002 TRP J 154 HIS 0.007 0.003 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (16956) covalent geometry : angle 0.61745 / 0.34 (23016) SS BOND : bond 0.00686 / 0.41 ( 12) SS BOND : angle 1.10741 / 0.70 ( 24) hydrogen bonds : bond 0.07575 / 5.08 ( 1152) hydrogen bonds : angle 5.41243 / 3.72 ( 3372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 0.574 Fit side-chains REVERT: A 171 LYS cc_start: 0.6279 (tttt) cc_final: 0.5504 (ttpt) REVERT: A 179 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8520 (p) REVERT: B 171 LYS cc_start: 0.6209 (tttt) cc_final: 0.5399 (ttpt) REVERT: C 63 ASP cc_start: 0.8261 (m-30) cc_final: 0.7904 (m-30) REVERT: C 162 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7284 (pptt) REVERT: C 171 LYS cc_start: 0.6384 (tttt) cc_final: 0.5610 (ttpt) REVERT: C 179 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8464 (p) REVERT: D 171 LYS cc_start: 0.6309 (tttt) cc_final: 0.5555 (ttpt) REVERT: E 171 LYS cc_start: 0.6335 (tttt) cc_final: 0.5573 (ttpt) REVERT: F 171 LYS cc_start: 0.6498 (tttt) cc_final: 0.5353 (pptt) REVERT: G 54 GLU cc_start: 0.8034 (pm20) cc_final: 0.7776 (pm20) REVERT: G 171 LYS cc_start: 0.6094 (tttt) cc_final: 0.5324 (ttpt) REVERT: G 174 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6936 (tt0) REVERT: H 125 GLU cc_start: 0.8226 (tt0) cc_final: 0.8004 (tt0) REVERT: H 171 LYS cc_start: 0.6186 (tttt) cc_final: 0.5516 (ttpt) REVERT: I 171 LYS cc_start: 0.6414 (tttt) cc_final: 0.5233 (pptt) REVERT: J 171 LYS cc_start: 0.6364 (tttt) cc_final: 0.5622 (ttpt) REVERT: K 41 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8184 (tmm-80) REVERT: K 54 GLU cc_start: 0.7915 (pm20) cc_final: 0.7616 (pm20) REVERT: K 171 LYS cc_start: 0.6352 (tttt) cc_final: 0.5643 (ttpt) REVERT: L 171 LYS cc_start: 0.6131 (tttt) cc_final: 0.5338 (ttpt) outliers start: 34 outliers final: 25 residues processed: 270 average time/residue: 0.7084 time to fit residues: 208.1887 Evaluate side-chains 277 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 41 ARG Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.183056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.170607 restraints weight = 47140.722| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.31 r_work: 0.3832 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16968 Z= 0.171 Angle : 0.583 4.596 23040 Z= 0.327 Chirality : 0.038 0.140 2532 Planarity : 0.005 0.043 2988 Dihedral : 4.209 15.119 2316 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.07 % Allowed : 11.61 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.18), residues: 2040 helix: 1.71 (0.12), residues: 1416 sheet: None (None), residues: 0 loop : 1.36 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 95 TYR 0.021 0.002 TYR E 123 PHE 0.017 0.002 PHE A 31 TRP 0.020 0.003 TRP H 154 HIS 0.006 0.002 HIS H 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (16956) covalent geometry : angle 0.58270 / 0.33 (23016) SS BOND : bond 0.00684 / 0.41 ( 12) SS BOND : angle 1.04911 / 0.66 ( 24) hydrogen bonds : bond 0.07263 / 4.87 ( 1152) hydrogen bonds : angle 5.38396 / 3.70 ( 3372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.748 Fit side-chains REVERT: A 171 LYS cc_start: 0.6146 (tttt) cc_final: 0.5248 (ttpt) REVERT: A 179 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 171 LYS cc_start: 0.5997 (tttt) cc_final: 0.5056 (ttpt) REVERT: C 41 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8331 (tmm-80) REVERT: C 171 LYS cc_start: 0.6343 (tttt) cc_final: 0.5461 (ttpt) REVERT: C 179 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8487 (p) REVERT: D 171 LYS cc_start: 0.6193 (tttt) cc_final: 0.5348 (ttpt) REVERT: E 171 LYS cc_start: 0.6175 (tttt) cc_final: 0.5306 (ttpt) REVERT: F 63 ASP cc_start: 0.8282 (m-30) cc_final: 0.7987 (m-30) REVERT: F 171 LYS cc_start: 0.6368 (tttt) cc_final: 0.5106 (pptt) REVERT: G 54 GLU cc_start: 0.8224 (pm20) cc_final: 0.7913 (pm20) REVERT: G 171 LYS cc_start: 0.5872 (tttt) cc_final: 0.4969 (ttpt) REVERT: G 174 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7077 (tt0) REVERT: H 125 GLU cc_start: 0.8376 (tt0) cc_final: 0.8145 (tt0) REVERT: H 171 LYS cc_start: 0.6103 (tttt) cc_final: 0.5323 (ttpt) REVERT: I 171 LYS cc_start: 0.6207 (tttt) cc_final: 0.5246 (ttpt) REVERT: J 171 LYS cc_start: 0.6233 (tttt) cc_final: 0.5381 (ttpt) REVERT: K 41 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8355 (tmm-80) REVERT: K 54 GLU cc_start: 0.8096 (pm20) cc_final: 0.7764 (pm20) REVERT: K 171 LYS cc_start: 0.6227 (tttt) cc_final: 0.5412 (ttpt) REVERT: L 171 LYS cc_start: 0.5945 (tttt) cc_final: 0.5018 (ttpt) outliers start: 36 outliers final: 28 residues processed: 270 average time/residue: 0.6925 time to fit residues: 203.6683 Evaluate side-chains 281 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 41 ARG Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 141 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 58 optimal weight: 0.0470 chunk 179 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.184941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.171213 restraints weight = 50110.034| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.39 r_work: 0.3826 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16968 Z= 0.144 Angle : 0.542 4.793 23040 Z= 0.305 Chirality : 0.037 0.133 2532 Planarity : 0.004 0.040 2988 Dihedral : 4.022 14.603 2316 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.90 % Allowed : 12.07 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.18), residues: 2040 helix: 1.95 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 1.40 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 95 TYR 0.018 0.002 TYR E 123 PHE 0.022 0.002 PHE A 31 TRP 0.024 0.003 TRP C 154 HIS 0.004 0.002 HIS H 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (16956) covalent geometry : angle 0.54154 / 0.30 (23016) SS BOND : bond 0.00593 / 0.36 ( 12) SS BOND : angle 1.04848 / 0.66 ( 24) hydrogen bonds : bond 0.06634 / 4.45 ( 1152) hydrogen bonds : angle 5.26932 / 3.63 ( 3372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.688 Fit side-chains REVERT: A 171 LYS cc_start: 0.6134 (tttt) cc_final: 0.5234 (ttpt) REVERT: A 179 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8446 (p) REVERT: B 171 LYS cc_start: 0.6018 (tttt) cc_final: 0.5118 (ttpt) REVERT: C 63 ASP cc_start: 0.8139 (m-30) cc_final: 0.7847 (m-30) REVERT: C 171 LYS cc_start: 0.6328 (tttt) cc_final: 0.5446 (ttpt) REVERT: C 179 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8468 (p) REVERT: D 171 LYS cc_start: 0.6173 (tttt) cc_final: 0.5310 (ttpt) REVERT: E 171 LYS cc_start: 0.6198 (tttt) cc_final: 0.5360 (ttpt) REVERT: F 171 LYS cc_start: 0.6306 (tttt) cc_final: 0.5063 (pptt) REVERT: F 179 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8461 (p) REVERT: G 171 LYS cc_start: 0.5945 (tttt) cc_final: 0.5052 (ttpt) REVERT: G 174 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: H 125 GLU cc_start: 0.8316 (tt0) cc_final: 0.8095 (tt0) REVERT: H 171 LYS cc_start: 0.6082 (tttt) cc_final: 0.5292 (ttpt) REVERT: H 179 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8429 (p) REVERT: I 41 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8308 (tmm-80) REVERT: I 171 LYS cc_start: 0.6140 (tttt) cc_final: 0.4897 (pptt) REVERT: J 171 LYS cc_start: 0.6198 (tttt) cc_final: 0.5353 (ttpt) REVERT: K 54 GLU cc_start: 0.8089 (pm20) cc_final: 0.7754 (pm20) REVERT: K 171 LYS cc_start: 0.6107 (tttt) cc_final: 0.5289 (ttpt) REVERT: L 171 LYS cc_start: 0.5918 (tttt) cc_final: 0.5033 (ttpt) outliers start: 33 outliers final: 25 residues processed: 260 average time/residue: 0.7078 time to fit residues: 200.5690 Evaluate side-chains 266 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 86 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.184351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170731 restraints weight = 49144.512| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.38 r_work: 0.3832 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16968 Z= 0.150 Angle : 0.554 5.209 23040 Z= 0.310 Chirality : 0.037 0.132 2532 Planarity : 0.004 0.040 2988 Dihedral : 4.041 14.624 2316 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.90 % Allowed : 12.01 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.18), residues: 2040 helix: 1.94 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 1.43 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 95 TYR 0.019 0.002 TYR E 123 PHE 0.019 0.002 PHE A 31 TRP 0.024 0.003 TRP C 154 HIS 0.004 0.002 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (16956) covalent geometry : angle 0.55326 / 0.31 (23016) SS BOND : bond 0.00605 / 0.36 ( 12) SS BOND : angle 1.06394 / 0.67 ( 24) hydrogen bonds : bond 0.06771 / 4.54 ( 1152) hydrogen bonds : angle 5.26915 / 3.63 ( 3372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6126.24 seconds wall clock time: 104 minutes 53.00 seconds (6293.00 seconds total)