Starting phenix.real_space_refine on Sat Jul 4 00:59:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cz0_46055/07_2026/9cz0_46055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cz0_46055/07_2026/9cz0_46055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cz0_46055/07_2026/9cz0_46055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cz0_46055/07_2026/9cz0_46055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cz0_46055/07_2026/9cz0_46055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cz0_46055/07_2026/9cz0_46055.map" } resolution = 1.86 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 36 5.16 5 C 10752 2.51 5 N 2736 2.21 5 O 3492 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: 17040 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1390 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Conformer: "B" Number of residues, atoms: 170, 1376 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1392 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Residues with excluded nonbonded symmetry interactions: 204 residue: pdb="FE FE A 201 " occ=0.50 residue: pdb="FE FE A 202 " occ=0.50 residue: pdb="FE FE B 201 " occ=0.50 residue: pdb="FE FE B 202 " occ=0.50 residue: pdb="FE FE C 201 " occ=0.50 residue: pdb="FE FE C 202 " occ=0.50 residue: pdb="FE FE D 201 " occ=0.50 residue: pdb="FE FE D 202 " occ=0.50 residue: pdb="FE FE E 201 " occ=0.50 residue: pdb="FE FE E 202 " occ=0.50 residue: pdb="FE FE F 201 " occ=0.50 residue: pdb="FE FE F 202 " occ=0.50 ... (remaining 192 not shown) Time building chain proxies: 1.71, per 1000 atoms: 0.10 Number of scatterers: 17040 At special positions: 0 Unit cell: (105.57, 109.02, 101.43, 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 36 16.00 O 3492 8.00 N 2736 7.00 C 10752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 15 through 43 removed outlier: 3.647A pdb=" N THR A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'A' and resid 104 through 131 Processing helix chain 'A' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.647A pdb=" N THR B 38 " --> pdb=" O TYR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 77 removed outlier: 3.892A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'B' and resid 104 through 131 Processing helix chain 'B' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.647A pdb=" N THR C 38 " --> pdb=" O TYR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'C' and resid 104 through 131 Processing helix chain 'C' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.647A pdb=" N THR D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'D' and resid 104 through 131 Processing helix chain 'D' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.646A pdb=" N THR E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'E' and resid 104 through 131 Processing helix chain 'E' and resid 134 through 161 removed outlier: 3.564A 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 43 removed outlier: 3.646A pdb=" N THR F 38 " --> pdb=" O TYR F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'F' and resid 104 through 131 Processing helix chain 'F' and resid 134 through 161 removed outlier: 3.562A 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 43 removed outlier: 3.647A pdb=" N THR G 38 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 4.591A 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 91 Processing helix chain 'G' and resid 104 through 131 Processing helix chain 'G' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.647A pdb=" N THR H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'H' and resid 104 through 131 Processing helix chain 'H' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.648A pdb=" N THR I 38 " --> pdb=" O TYR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.892A pdb=" N ALA I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'I' and resid 104 through 131 Processing helix chain 'I' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.646A pdb=" N THR J 38 " --> pdb=" O TYR J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 77 removed outlier: 3.892A pdb=" N ALA J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'J' and resid 104 through 131 Processing helix chain 'J' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.646A pdb=" N THR K 38 " --> pdb=" O TYR K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 4.590A 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 91 Processing helix chain 'K' and resid 104 through 131 Processing helix chain 'K' and resid 134 through 161 removed outlier: 3.563A 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 43 removed outlier: 3.647A pdb=" N THR L 38 " --> pdb=" O TYR L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 77 removed outlier: 3.891A pdb=" N ALA L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 4.589A 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 91 Processing helix chain 'L' and resid 104 through 131 Processing helix chain 'L' and resid 134 through 161 removed outlier: 3.563A pdb=" N GLU L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 182 1188 hydrogen bonds defined for protein. 3468 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: 2.00 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5415 1.34 - 1.46: 3916 1.46 - 1.58: 7721 1.58 - 1.71: 0 1.71 - 1.83: 36 Bond restraints: 17088 Sorted by residual: bond pdb=" CB BTRP E 154 " pdb=" CG BTRP E 154 " ideal model delta sigma weight residual 1.498 1.438 0.060 3.10e-02 1.04e+03 3.70e+00 bond pdb=" CB BTRP K 154 " pdb=" CG BTRP K 154 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.67e+00 bond pdb=" CB BTRP H 154 " pdb=" CG BTRP H 154 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.64e+00 bond pdb=" CB BTRP I 154 " pdb=" CG BTRP I 154 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.62e+00 bond pdb=" CB BTRP B 154 " pdb=" CG BTRP B 154 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.60e+00 ... (remaining 17083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 21084 1.10 - 2.20: 1640 2.20 - 3.30: 352 3.30 - 4.40: 65 4.40 - 5.50: 43 Bond angle restraints: 23184 Sorted by residual: angle pdb=" CA TYR E 123 " pdb=" CB TYR E 123 " pdb=" CG TYR E 123 " ideal model delta sigma weight residual 113.90 109.46 4.44 1.80e+00 3.09e-01 6.09e+00 angle pdb=" CA TYR K 123 " pdb=" CB TYR K 123 " pdb=" CG TYR K 123 " ideal model delta sigma weight residual 113.90 109.48 4.42 1.80e+00 3.09e-01 6.04e+00 angle pdb=" CA TYR A 123 " pdb=" CB TYR A 123 " pdb=" CG TYR A 123 " ideal model delta sigma weight residual 113.90 109.48 4.42 1.80e+00 3.09e-01 6.03e+00 angle pdb=" CA TYR J 123 " pdb=" CB TYR J 123 " pdb=" CG TYR J 123 " ideal model delta sigma weight residual 113.90 109.48 4.42 1.80e+00 3.09e-01 6.03e+00 angle pdb=" CA TYR F 123 " pdb=" CB TYR F 123 " pdb=" CG TYR F 123 " ideal model delta sigma weight residual 113.90 109.49 4.41 1.80e+00 3.09e-01 6.01e+00 ... (remaining 23179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 9156 16.64 - 33.28: 816 33.28 - 49.92: 240 49.92 - 66.56: 24 66.56 - 83.20: 24 Dihedral angle restraints: 10260 sinusoidal: 4224 harmonic: 6036 Sorted by residual: dihedral pdb=" CA PHE E 167 " pdb=" C PHE E 167 " pdb=" N ARG E 168 " pdb=" CA ARG E 168 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA PHE K 167 " pdb=" C PHE K 167 " pdb=" N ARG K 168 " pdb=" CA ARG K 168 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA PHE H 167 " pdb=" C PHE H 167 " pdb=" N ARG H 168 " pdb=" CA ARG H 168 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 10257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 696 0.030 - 0.059: 1111 0.059 - 0.089: 523 0.089 - 0.119: 148 0.119 - 0.149: 42 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA PRO K 103 " pdb=" N PRO K 103 " pdb=" C PRO K 103 " pdb=" CB PRO K 103 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" C PRO E 103 " pdb=" CB PRO E 103 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA PRO J 103 " pdb=" N PRO J 103 " pdb=" C PRO J 103 " pdb=" CB PRO J 103 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 2517 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 86 " 0.126 9.50e-02 1.11e+02 5.66e-02 2.01e+00 pdb=" NE ARG L 86 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG L 86 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG L 86 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG L 86 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 86 " -0.126 9.50e-02 1.11e+02 5.66e-02 2.00e+00 pdb=" NE ARG J 86 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG J 86 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG J 86 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG J 86 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 86 " -0.126 9.50e-02 1.11e+02 5.64e-02 2.00e+00 pdb=" NE ARG E 86 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG E 86 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 86 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 86 " -0.006 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 252 2.52 - 3.11: 13398 3.11 - 3.71: 30359 3.71 - 4.30: 43002 4.30 - 4.90: 70411 Nonbonded interactions: 157422 Sorted by model distance: nonbonded pdb=" OE2 GLU C 148 " pdb="FE FE C 201 " model vdw 1.919 3.000 nonbonded pdb=" OE2 GLU J 148 " pdb="FE FE J 201 " model vdw 1.919 3.000 nonbonded pdb=" OE2 GLU B 148 " pdb="FE FE B 201 " model vdw 1.919 3.000 nonbonded pdb=" OE2 GLU D 148 " pdb="FE FE D 201 " model vdw 1.920 3.000 nonbonded pdb=" OE2 GLU I 148 " pdb="FE FE I 201 " model vdw 1.920 3.000 ... (remaining 157417 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=0.99 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: 7.210 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: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 17088 Z= 0.358 Angle : 0.701 5.495 23184 Z= 0.372 Chirality : 0.054 0.149 2520 Planarity : 0.006 0.057 3000 Dihedral : 14.064 83.200 6396 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: 1.34 (0.18), residues: 2028 helix: 0.99 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 0.97 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 86 TYR 0.023 0.003 TYR B 123 PHE 0.008 0.003 PHE G 88 HIS 0.009 0.002 HIS F 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.36 (17088) covalent geometry : angle 0.70084 / 0.37 (23184) hydrogen bonds : bond 0.14773 / 10.17 ( 1188) hydrogen bonds : angle 6.58563 / 4.75 ( 3468) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.550 Fit side-chains REVERT: A 17 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8118 (mp0) REVERT: B 17 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8066 (mp0) REVERT: C 17 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8177 (mp0) REVERT: D 17 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8238 (mp0) REVERT: E 17 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8063 (mp0) REVERT: F 17 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8171 (mp0) REVERT: H 17 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7978 (mp0) REVERT: K 17 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8137 (mm-30) REVERT: L 17 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8148 (mp0) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.8589 time to fit residues: 320.6380 Evaluate side-chains 332 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 0.7980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS B 166 HIS C 166 HIS D 166 HIS F 166 HIS G 166 HIS H 166 HIS I 166 HIS J 166 HIS K 166 HIS L 166 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120041 restraints weight = 28233.027| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.21 r_work: 0.3174 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17088 Z= 0.167 Angle : 0.569 4.485 23184 Z= 0.320 Chirality : 0.039 0.132 2520 Planarity : 0.004 0.025 3000 Dihedral : 4.156 15.421 2304 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 6.21 % Favored : 93.33 % 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: 2.76 (0.19), residues: 2028 helix: 2.07 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.43 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 41 TYR 0.023 0.002 TYR L 123 PHE 0.017 0.002 PHE A 31 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (17088) covalent geometry : angle 0.56894 / 0.32 (23184) hydrogen bonds : bond 0.07290 / 5.00 ( 1188) hydrogen bonds : angle 5.54212 / 3.99 ( 3468) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 392 time to evaluate : 0.666 Fit side-chains REVERT: A 54 GLU cc_start: 0.8703 (tt0) cc_final: 0.8273 (pp20) REVERT: G 148 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8426 (mm-30) REVERT: H 15 ASP cc_start: 0.8533 (t0) cc_final: 0.8299 (t0) REVERT: J 162 LYS cc_start: 0.7929 (ttpp) cc_final: 0.7708 (tmtt) outliers start: 8 outliers final: 2 residues processed: 392 average time/residue: 0.8635 time to fit residues: 362.7005 Evaluate side-chains 361 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain F residue 174 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 136 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN C 42 ASN E 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117476 restraints weight = 28834.868| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.52 r_work: 0.3219 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17088 Z= 0.171 Angle : 0.562 4.670 23184 Z= 0.313 Chirality : 0.039 0.124 2520 Planarity : 0.004 0.026 3000 Dihedral : 4.104 15.627 2304 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 0.40 % Allowed : 8.10 % Favored : 91.49 % 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: 2.90 (0.19), residues: 2028 helix: 2.12 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.66 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 86 TYR 0.020 0.002 TYR B 123 PHE 0.012 0.002 PHE B 31 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (17088) covalent geometry : angle 0.56162 / 0.31 (23184) hydrogen bonds : bond 0.07322 / 5.02 ( 1188) hydrogen bonds : angle 5.43494 / 3.91 ( 3468) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 367 time to evaluate : 0.482 Fit side-chains REVERT: A 54 GLU cc_start: 0.8560 (tt0) cc_final: 0.7896 (pp20) REVERT: D 162 LYS cc_start: 0.7777 (tmtt) cc_final: 0.7560 (tmtt) REVERT: E 162 LYS cc_start: 0.7801 (tttt) cc_final: 0.7596 (tmtt) REVERT: I 50 GLU cc_start: 0.8038 (tp30) cc_final: 0.7830 (tp30) outliers start: 7 outliers final: 2 residues processed: 367 average time/residue: 0.8491 time to fit residues: 334.1423 Evaluate side-chains 356 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 354 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain G residue 174 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108635 restraints weight = 23354.242| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.43 r_work: 0.3075 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17088 Z= 0.197 Angle : 0.594 4.921 23184 Z= 0.330 Chirality : 0.040 0.130 2520 Planarity : 0.004 0.032 3000 Dihedral : 4.191 16.571 2304 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.52 % Allowed : 8.91 % Favored : 90.57 % 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: 2.78 (0.19), residues: 2028 helix: 1.99 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.73 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.022 0.002 TYR B 123 PHE 0.011 0.002 PHE B 31 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (17088) covalent geometry : angle 0.59384 / 0.33 (23184) hydrogen bonds : bond 0.07712 / 5.29 ( 1188) hydrogen bonds : angle 5.45952 / 3.93 ( 3468) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 357 time to evaluate : 0.439 Fit side-chains REVERT: A 54 GLU cc_start: 0.8367 (tt0) cc_final: 0.7639 (pp20) REVERT: D 162 LYS cc_start: 0.7714 (tmtt) cc_final: 0.7411 (tmtt) REVERT: G 102 GLU cc_start: 0.7534 (mp0) cc_final: 0.7331 (mp0) REVERT: I 50 GLU cc_start: 0.7951 (tp30) cc_final: 0.7751 (tp30) outliers start: 9 outliers final: 2 residues processed: 357 average time/residue: 0.8968 time to fit residues: 342.6188 Evaluate side-chains 347 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 345 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain G residue 174 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 200 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 178 optimal weight: 0.1980 chunk 197 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 143 optimal weight: 0.0870 chunk 129 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 ASN E 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112379 restraints weight = 24024.694| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.45 r_work: 0.3135 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17088 Z= 0.153 Angle : 0.539 4.500 23184 Z= 0.299 Chirality : 0.037 0.122 2520 Planarity : 0.004 0.025 3000 Dihedral : 4.016 14.946 2304 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.11 % Allowed : 9.48 % Favored : 90.40 % 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: 3.10 (0.19), residues: 2028 helix: 2.25 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.80 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 86 TYR 0.022 0.002 TYR G 75 PHE 0.016 0.002 PHE J 31 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (17088) covalent geometry : angle 0.53883 / 0.30 (23184) hydrogen bonds : bond 0.06789 / 4.66 ( 1188) hydrogen bonds : angle 5.30706 / 3.82 ( 3468) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 0.460 Fit side-chains REVERT: A 54 GLU cc_start: 0.8392 (tt0) cc_final: 0.7693 (pp20) REVERT: D 162 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7388 (tmtt) REVERT: G 102 GLU cc_start: 0.7513 (mp0) cc_final: 0.7286 (mp0) REVERT: H 54 GLU cc_start: 0.8265 (tt0) cc_final: 0.7703 (tp30) REVERT: J 162 LYS cc_start: 0.7587 (ttpp) cc_final: 0.7308 (tmtt) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.8410 time to fit residues: 333.6439 Evaluate side-chains 363 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 181 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 177 optimal weight: 0.1980 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN E 42 ASN I 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110543 restraints weight = 24080.989| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.46 r_work: 0.3102 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17088 Z= 0.172 Angle : 0.562 4.638 23184 Z= 0.312 Chirality : 0.038 0.123 2520 Planarity : 0.004 0.024 3000 Dihedral : 4.074 15.501 2304 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 9.77 % Favored : 89.89 % 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: 2.99 (0.19), residues: 2028 helix: 2.15 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.79 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 86 TYR 0.020 0.002 TYR B 123 PHE 0.012 0.002 PHE B 31 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (17088) covalent geometry : angle 0.56246 / 0.31 (23184) hydrogen bonds : bond 0.07230 / 4.96 ( 1188) hydrogen bonds : angle 5.34361 / 3.85 ( 3468) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 367 time to evaluate : 0.614 Fit side-chains REVERT: A 54 GLU cc_start: 0.8367 (tt0) cc_final: 0.7647 (pp20) REVERT: D 162 LYS cc_start: 0.7680 (tmtt) cc_final: 0.7343 (tmtt) REVERT: G 102 GLU cc_start: 0.7520 (mp0) cc_final: 0.7295 (mp0) outliers start: 6 outliers final: 2 residues processed: 367 average time/residue: 0.8763 time to fit residues: 344.3392 Evaluate side-chains 349 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 347 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain G residue 174 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 159 optimal weight: 0.9990 chunk 127 optimal weight: 0.0470 chunk 65 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 73 optimal weight: 0.0270 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN C 42 ASN E 42 ASN I 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121500 restraints weight = 28689.428| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.51 r_work: 0.3284 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17088 Z= 0.144 Angle : 0.529 4.931 23184 Z= 0.293 Chirality : 0.037 0.117 2520 Planarity : 0.003 0.024 3000 Dihedral : 3.927 14.246 2304 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.11 % Allowed : 9.94 % Favored : 89.94 % 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: 3.16 (0.19), residues: 2028 helix: 2.29 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 1.79 (0.31), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 41 TYR 0.018 0.002 TYR L 123 PHE 0.017 0.002 PHE D 31 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (17088) covalent geometry : angle 0.52946 / 0.29 (23184) hydrogen bonds : bond 0.06440 / 4.42 ( 1188) hydrogen bonds : angle 5.23521 / 3.77 ( 3468) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.711 Fit side-chains REVERT: A 54 GLU cc_start: 0.8513 (tt0) cc_final: 0.7824 (pp20) REVERT: D 162 LYS cc_start: 0.7776 (tmtt) cc_final: 0.7469 (tmtt) REVERT: G 102 GLU cc_start: 0.7526 (mp0) cc_final: 0.7288 (mp0) REVERT: J 87 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7671 (pt0) REVERT: J 102 GLU cc_start: 0.7559 (mp0) cc_final: 0.7345 (mp0) outliers start: 2 outliers final: 0 residues processed: 367 average time/residue: 0.8923 time to fit residues: 351.1259 Evaluate side-chains 360 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.0270 chunk 67 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN E 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130606 restraints weight = 22766.514| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.26 r_work: 0.3485 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (16 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17088 Z= 0.143 Angle : 0.525 4.956 23184 Z= 0.290 Chirality : 0.036 0.115 2520 Planarity : 0.003 0.031 3000 Dihedral : 3.870 13.639 2304 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.17 % Allowed : 10.40 % Favored : 89.43 % 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: 3.16 (0.19), residues: 2028 helix: 2.29 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 1.80 (0.31), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 41 TYR 0.019 0.002 TYR G 75 PHE 0.016 0.002 PHE D 31 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (17088) covalent geometry : angle 0.52479 / 0.29 (23184) hydrogen bonds : bond 0.06323 / 4.34 ( 1188) hydrogen bonds : angle 5.19037 / 3.73 ( 3468) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 367 time to evaluate : 0.684 Fit side-chains REVERT: A 54 GLU cc_start: 0.8580 (tt0) cc_final: 0.8007 (pp20) REVERT: H 54 GLU cc_start: 0.8474 (tt0) cc_final: 0.8010 (tp30) REVERT: J 162 LYS cc_start: 0.7847 (tttp) cc_final: 0.7574 (tmtt) outliers start: 3 outliers final: 1 residues processed: 368 average time/residue: 0.8993 time to fit residues: 354.4379 Evaluate side-chains 360 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 159 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 182 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 184 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN E 42 ASN I 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123693 restraints weight = 25757.529| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.41 r_work: 0.3318 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17088 Z= 0.148 Angle : 0.534 5.312 23184 Z= 0.295 Chirality : 0.036 0.115 2520 Planarity : 0.003 0.025 3000 Dihedral : 3.899 13.666 2304 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % 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: 3.17 (0.19), residues: 2028 helix: 2.30 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.83 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 41 TYR 0.018 0.002 TYR L 123 PHE 0.015 0.002 PHE D 31 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (17088) covalent geometry : angle 0.53396 / 0.30 (23184) hydrogen bonds : bond 0.06482 / 4.45 ( 1188) hydrogen bonds : angle 5.19071 / 3.74 ( 3468) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.596 Fit side-chains REVERT: A 54 GLU cc_start: 0.8480 (tt0) cc_final: 0.7828 (pp20) REVERT: H 54 GLU cc_start: 0.8397 (tt0) cc_final: 0.7888 (tp30) REVERT: J 162 LYS cc_start: 0.7643 (tttp) cc_final: 0.7340 (tmtt) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.9197 time to fit residues: 356.0170 Evaluate side-chains 353 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 154 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN E 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110003 restraints weight = 18808.248| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.28 r_work: 0.3110 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17088 Z= 0.201 Angle : 0.603 5.374 23184 Z= 0.335 Chirality : 0.040 0.122 2520 Planarity : 0.004 0.032 3000 Dihedral : 4.138 15.824 2304 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.06 % Allowed : 10.52 % Favored : 89.43 % 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: 2.84 (0.19), residues: 2028 helix: 2.01 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.84 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 86 TYR 0.023 0.002 TYR A 123 PHE 0.010 0.002 PHE J 31 HIS 0.006 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (17088) covalent geometry : angle 0.60325 / 0.33 (23184) hydrogen bonds : bond 0.07615 / 5.22 ( 1188) hydrogen bonds : angle 5.34447 / 3.85 ( 3468) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.634 Fit side-chains REVERT: E 87 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7597 (pt0) REVERT: G 102 GLU cc_start: 0.7482 (mp0) cc_final: 0.7253 (mp0) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.9285 time to fit residues: 350.8504 Evaluate side-chains 346 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 20 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 54 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 ASN E 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108843 restraints weight = 27128.472| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.55 r_work: 0.3077 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17088 Z= 0.190 Angle : 0.594 5.825 23184 Z= 0.330 Chirality : 0.040 0.122 2520 Planarity : 0.004 0.029 3000 Dihedral : 4.166 16.042 2304 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 10.46 % Favored : 89.37 % 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: 2.81 (0.19), residues: 2028 helix: 1.98 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.83 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.022 0.002 TYR B 123 PHE 0.010 0.002 PHE J 31 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (17088) covalent geometry : angle 0.59447 / 0.33 (23184) hydrogen bonds : bond 0.07462 / 5.12 ( 1188) hydrogen bonds : angle 5.33336 / 3.84 ( 3468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9020.32 seconds wall clock time: 153 minutes 29.91 seconds (9209.91 seconds total)