Starting phenix.real_space_refine on Sun Aug 24 05:31:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cz0_46055/08_2025/9cz0_46055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cz0_46055/08_2025/9cz0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cz0_46055/08_2025/9cz0_46055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cz0_46055/08_2025/9cz0_46055.map" model { file = "/net/cci-nas-00/data/ceres_data/9cz0_46055/08_2025/9cz0_46055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cz0_46055/08_2025/9cz0_46055.cif" } 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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2.07, per 1000 atoms: 0.12 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: 1.23 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.29 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: 1.85 Time building geometry restraints manager: 1.68 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 2.260 nonbonded pdb=" OE2 GLU J 148 " pdb="FE FE J 201 " model vdw 1.919 2.260 nonbonded pdb=" OE2 GLU B 148 " pdb="FE FE B 201 " model vdw 1.919 2.260 nonbonded pdb=" OE2 GLU D 148 " pdb="FE FE D 201 " model vdw 1.920 2.260 nonbonded pdb=" OE2 GLU I 148 " pdb="FE FE I 201 " model vdw 1.920 2.260 ... (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: 8.350 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 12.980 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: 0.000 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 aren 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 covalent geometry : bond 0.00863 (17088) covalent geometry : angle 0.70084 (23184) hydrogen bonds : bond 0.14773 ( 1188) hydrogen bonds : angle 6.58563 ( 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 : 0.546 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: 0.9814 time to fit residues: 365.0033 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 : 0.615 ------------------------------------------------------------------------------- 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: 0.6980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3581 r_free = 0.3581 target = 0.139127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119292 restraints weight = 28725.047| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.23 r_work: 0.3172 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.95 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 = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1566 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= 0.156 Angle : 0.547 4.562 23184 Z= 0.307 Chirality : 0.038 0.125 2520 Planarity : 0.004 0.023 3000 Dihedral : 4.121 14.941 2304 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 6.32 % Favored : 93.22 % 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 aren not related in a simple way. whole: 2.83 (0.19), residues: 2028 helix: 2.13 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.44 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 41 TYR 0.019 0.002 TYR A 123 PHE 0.017 0.002 PHE A 31 HIS 0.003 0.001 HIS L 166 Details of bonding type rmsd covalent geometry : bond 0.00303 (17088) covalent geometry : angle 0.54740 (23184) hydrogen bonds : bond 0.07050 ( 1188) hydrogen bonds : angle 5.51779 ( 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 399 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 391 time to evaluate : 0.604 Fit side-chains REVERT: A 54 GLU cc_start: 0.8745 (tt0) cc_final: 0.8318 (pp20) REVERT: H 15 ASP cc_start: 0.8517 (t0) cc_final: 0.8281 (t0) REVERT: J 162 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7728 (tmtt) outliers start: 8 outliers final: 2 residues processed: 391 average time/residue: 0.9296 time to fit residues: 388.7592 Evaluate side-chains 363 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 361 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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: 5.9990 chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN C 42 ASN E 42 ASN E 166 HIS I 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110229 restraints weight = 26512.109| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.48 r_work: 0.3153 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17088 Z= 0.242 Angle : 0.642 5.440 23184 Z= 0.356 Chirality : 0.044 0.139 2520 Planarity : 0.005 0.048 3000 Dihedral : 4.320 17.553 2304 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.86 % Allowed : 8.05 % Favored : 91.09 % 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 aren not related in a simple way. whole: 2.58 (0.19), residues: 2028 helix: 1.85 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.63 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 86 TYR 0.024 0.003 TYR A 123 PHE 0.009 0.002 PHE B 31 HIS 0.007 0.002 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00539 (17088) covalent geometry : angle 0.64186 (23184) hydrogen bonds : bond 0.08235 ( 1188) hydrogen bonds : angle 5.60489 ( 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 372 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 357 time to evaluate : 0.425 Fit side-chains REVERT: A 54 GLU cc_start: 0.8506 (tt0) cc_final: 0.7804 (pp20) REVERT: B 174 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7570 (tt0) outliers start: 15 outliers final: 4 residues processed: 357 average time/residue: 1.0754 time to fit residues: 409.5391 Evaluate side-chains 348 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 343 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain K residue 17 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: 1.9990 chunk 85 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115747 restraints weight = 23774.997| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.39 r_work: 0.3206 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17088 Z= 0.176 Angle : 0.573 4.729 23184 Z= 0.319 Chirality : 0.039 0.131 2520 Planarity : 0.004 0.027 3000 Dihedral : 4.178 16.378 2304 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.40 % Allowed : 8.97 % Favored : 90.63 % 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 aren not related in a simple way. whole: 2.85 (0.19), residues: 2028 helix: 2.04 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.76 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 86 TYR 0.022 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 covalent geometry : bond 0.00362 (17088) covalent geometry : angle 0.57312 (23184) hydrogen bonds : bond 0.07403 ( 1188) hydrogen bonds : angle 5.44011 ( 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 371 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 364 time to evaluate : 0.642 Fit side-chains REVERT: A 54 GLU cc_start: 0.8488 (tt0) cc_final: 0.7799 (pp20) REVERT: B 174 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7561 (tt0) outliers start: 7 outliers final: 2 residues processed: 364 average time/residue: 0.9764 time to fit residues: 379.3253 Evaluate side-chains 361 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 358 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain J 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: 7.9990 chunk 76 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.133967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112355 restraints weight = 22511.203| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.36 r_work: 0.3190 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17088 Z= 0.203 Angle : 0.604 5.093 23184 Z= 0.335 Chirality : 0.041 0.133 2520 Planarity : 0.004 0.033 3000 Dihedral : 4.235 16.915 2304 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.57 % Allowed : 8.79 % Favored : 90.63 % 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 aren not related in a simple way. whole: 2.73 (0.19), residues: 2028 helix: 1.93 (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 0.004 0.000 ARG B 86 TYR 0.024 0.002 TYR B 123 PHE 0.010 0.002 PHE B 31 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00434 (17088) covalent geometry : angle 0.60418 (23184) hydrogen bonds : bond 0.07797 ( 1188) hydrogen bonds : angle 5.48168 ( 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 367 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 357 time to evaluate : 0.555 Fit side-chains REVERT: A 54 GLU cc_start: 0.8490 (tt0) cc_final: 0.7802 (pp20) REVERT: B 174 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: D 162 LYS cc_start: 0.7755 (tmtt) cc_final: 0.7498 (tmtt) outliers start: 10 outliers final: 2 residues processed: 358 average time/residue: 0.9401 time to fit residues: 358.9633 Evaluate side-chains 347 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 344 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain G residue 174 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 181 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN C 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112878 restraints weight = 22755.433| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.36 r_work: 0.3199 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1827 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= 0.191 Angle : 0.593 4.921 23184 Z= 0.329 Chirality : 0.040 0.131 2520 Planarity : 0.004 0.030 3000 Dihedral : 4.209 16.628 2304 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.52 % Allowed : 9.14 % Favored : 90.34 % 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 aren not related in a simple way. whole: 2.81 (0.19), residues: 2028 helix: 1.99 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : 1.81 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.023 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 covalent geometry : bond 0.00404 (17088) covalent geometry : angle 0.59254 (23184) hydrogen bonds : bond 0.07618 ( 1188) hydrogen bonds : angle 5.44224 ( 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 368 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 359 time to evaluate : 0.720 Fit side-chains REVERT: B 174 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: D 162 LYS cc_start: 0.7772 (tmtt) cc_final: 0.7509 (tmtt) outliers start: 9 outliers final: 2 residues processed: 359 average time/residue: 1.1000 time to fit residues: 421.0600 Evaluate side-chains 351 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 348 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 GLU 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.1685 > 50: distance: 6 - 19: 3.001 distance: 64 - 88: 13.929 distance: 68 - 93: 13.461 distance: 74 - 118: 10.688 distance: 82 - 88: 14.213 distance: 83 - 129: 7.717 distance: 88 - 89: 28.833 distance: 89 - 90: 16.732 distance: 89 - 92: 10.882 distance: 90 - 91: 18.571 distance: 90 - 93: 13.881 distance: 91 - 138: 11.543 distance: 93 - 96: 19.610 distance: 93 - 107: 16.916 distance: 94 - 95: 37.324 distance: 94 - 96: 8.296 distance: 94 - 107: 7.193 distance: 94 - 118: 16.604 distance: 95 - 147: 31.634 distance: 96 - 97: 6.599 distance: 97 - 98: 8.506 distance: 98 - 99: 6.082 distance: 98 - 100: 6.819 distance: 99 - 101: 4.787 distance: 100 - 103: 4.595 distance: 103 - 105: 4.475 distance: 104 - 106: 4.177 distance: 105 - 106: 3.750 distance: 107 - 108: 12.531 distance: 108 - 109: 5.002 distance: 109 - 110: 4.196 distance: 109 - 111: 7.320 distance: 110 - 112: 3.929 distance: 112 - 113: 4.552 distance: 113 - 115: 4.605 distance: 114 - 116: 3.822 distance: 115 - 117: 5.416 distance: 116 - 117: 7.312 distance: 118 - 119: 11.337 distance: 119 - 120: 11.360 distance: 119 - 122: 4.700 distance: 120 - 121: 13.350 distance: 120 - 129: 22.997 distance: 121 - 155: 22.117 distance: 122 - 123: 8.645 distance: 123 - 124: 11.704 distance: 123 - 125: 7.836 distance: 124 - 126: 13.102 distance: 125 - 127: 8.938 distance: 126 - 128: 3.736 distance: 127 - 128: 9.848 distance: 129 - 130: 8.837 distance: 130 - 131: 11.396 distance: 130 - 133: 16.931 distance: 131 - 132: 7.668 distance: 131 - 138: 8.932 distance: 132 - 163: 19.133 distance: 133 - 134: 17.405 distance: 134 - 135: 12.042 distance: 135 - 136: 5.647 distance: 135 - 137: 32.254 distance: 138 - 139: 17.367 distance: 139 - 140: 32.905 distance: 139 - 142: 11.494 distance: 140 - 141: 28.717 distance: 140 - 147: 25.715 distance: 141 - 170: 12.524 distance: 142 - 143: 15.289 distance: 143 - 144: 16.290 distance: 144 - 145: 17.519 distance: 144 - 146: 8.563 distance: 147 - 148: 21.882 distance: 148 - 149: 13.065 distance: 148 - 151: 15.825 distance: 149 - 150: 33.477 distance: 149 - 155: 33.741 distance: 151 - 152: 21.053 distance: 152 - 153: 12.801 distance: 152 - 154: 11.417 distance: 155 - 156: 23.611 distance: 156 - 157: 15.594 distance: 156 - 159: 19.556 distance: 157 - 158: 21.849 distance: 157 - 163: 19.821 distance: 159 - 160: 24.948 distance: 160 - 161: 21.660 distance: 160 - 162: 22.549 distance: 163 - 164: 9.383 distance: 164 - 165: 12.414 distance: 164 - 167: 20.082 distance: 165 - 166: 33.677 distance: 165 - 170: 33.520 distance: 167 - 168: 12.128 distance: 167 - 169: 5.589 distance: 170 - 171: 5.601 distance: 171 - 172: 8.937 distance: 172 - 173: 20.985 distance: 172 - 174: 28.806 distance: 174 - 175: 8.826 distance: 175 - 176: 9.863 distance: 175 - 178: 5.274 distance: 176 - 177: 13.666 distance: 176 - 183: 10.645 distance: 178 - 179: 13.875 distance: 179 - 180: 17.298 distance: 180 - 181: 8.383 distance: 181 - 182: 19.497