Starting phenix.real_space_refine on Thu Oct 22 17:11:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9neq_49330/10_2026/9neq_49330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9neq_49330/10_2026/9neq_49330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9neq_49330/10_2026/9neq_49330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9neq_49330/10_2026/9neq_49330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9neq_49330/10_2026/9neq_49330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9neq_49330/10_2026/9neq_49330.map" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.048 sd= 0.440 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: 3 Type Number sf(0) Gaussians C 864 2.51 5 N 224 2.21 5 O 224 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1312 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 A 1 " pdbres="LEU A 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 B 1 " pdbres="LEU B 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 C 1 " pdbres="LEU C 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQ4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 D 1 " pdbres="LEU D 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 E 1 " pdbres="LEU E 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 F 1 " pdbres="LEU F 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQ4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 G 1 " pdbres="LEU G 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 H 1 " pdbres="LEU H 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 I 1 " pdbres="LEU I 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQ4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 J 1 " pdbres="LEU J 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 K 1 " pdbres="LEU K 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 L 1 " pdbres="LEU L 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQ4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 M 1 " pdbres="LEU M 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 N 1 " pdbres="LEU N 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 O 1 " pdbres="LEU O 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQ4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 P 1 " pdbres="LEU P 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 Q 1 " pdbres="LEU Q 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 R 1 " pdbres="LEU R 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQ4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 S 1 " pdbres="LEU S 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 T 1 " pdbres="LEU T 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 U 1 " pdbres="LEU U 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQ4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 V 1 " pdbres="LEU V 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 W 1 " pdbres="LEU W 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 49 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="UQ4 X 1 " pdbres="LEU X 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQ4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.25, per 1000 atoms: 0.19 Number of scatterers: 1312 At special positions: 0 Unit cell: (55.59, 62.13, 30.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 224 8.00 N 224 7.00 C 864 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.11 Conformation dependent library (CDL) restraints added in 10.9 milliseconds 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.25: 160 1.25 - 1.32: 64 1.32 - 1.39: 264 1.39 - 1.46: 192 1.46 - 1.54: 640 Bond restraints: 1320 Sorted by residual: bond pdb=" C53 UQ4 W 1 " pdb=" N52 UQ4 W 1 " ideal model delta sigma weight residual 1.342 1.511 -0.169 2.00e-02 2.50e+03 7.11e+01 bond pdb=" C53 UQ4 K 1 " pdb=" N52 UQ4 K 1 " ideal model delta sigma weight residual 1.342 1.511 -0.169 2.00e-02 2.50e+03 7.11e+01 bond pdb=" C53 UQ4 N 1 " pdb=" N52 UQ4 N 1 " ideal model delta sigma weight residual 1.342 1.511 -0.169 2.00e-02 2.50e+03 7.10e+01 bond pdb=" C53 UQ4 E 1 " pdb=" N52 UQ4 E 1 " ideal model delta sigma weight residual 1.342 1.511 -0.169 2.00e-02 2.50e+03 7.10e+01 bond pdb=" C53 UQ4 B 1 " pdb=" N52 UQ4 B 1 " ideal model delta sigma weight residual 1.342 1.510 -0.168 2.00e-02 2.50e+03 7.09e+01 ... (remaining 1315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 1344 1.78 - 3.57: 208 3.57 - 5.35: 104 5.35 - 7.14: 72 7.14 - 8.92: 24 Bond angle restraints: 1752 Sorted by residual: angle pdb=" C50 UQ4 Q 101 " pdb=" C02 UQ4 Q 101 " pdb=" O01 UQ4 Q 101 " ideal model delta sigma weight residual 126.87 117.95 8.92 3.00e+00 1.11e-01 8.85e+00 angle pdb=" C50 UQ4 H 101 " pdb=" C02 UQ4 H 101 " pdb=" O01 UQ4 H 101 " ideal model delta sigma weight residual 126.87 117.95 8.92 3.00e+00 1.11e-01 8.85e+00 angle pdb=" C50 UQ4 K 101 " pdb=" C02 UQ4 K 101 " pdb=" O01 UQ4 K 101 " ideal model delta sigma weight residual 126.87 117.97 8.90 3.00e+00 1.11e-01 8.80e+00 angle pdb=" C50 UQ4 W 101 " pdb=" C02 UQ4 W 101 " pdb=" O01 UQ4 W 101 " ideal model delta sigma weight residual 126.87 117.97 8.90 3.00e+00 1.11e-01 8.80e+00 angle pdb=" C50 UQ4 B 101 " pdb=" C02 UQ4 B 101 " pdb=" O01 UQ4 B 101 " ideal model delta sigma weight residual 126.87 117.97 8.90 3.00e+00 1.11e-01 8.79e+00 ... (remaining 1747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.54: 384 14.54 - 29.08: 64 29.08 - 43.62: 64 43.62 - 58.16: 24 58.16 - 72.70: 16 Dihedral angle restraints: 552 sinusoidal: 288 harmonic: 264 Sorted by residual: dihedral pdb=" CA LEU E 4 " pdb=" CB LEU E 4 " pdb=" CG LEU E 4 " pdb=" CD1 LEU E 4 " ideal model delta sinusoidal sigma weight residual 180.00 144.08 35.92 3 1.50e+01 4.44e-03 6.19e+00 dihedral pdb=" CA LEU N 4 " pdb=" CB LEU N 4 " pdb=" CG LEU N 4 " pdb=" CD1 LEU N 4 " ideal model delta sinusoidal sigma weight residual 180.00 144.08 35.92 3 1.50e+01 4.44e-03 6.19e+00 dihedral pdb=" CA LEU K 4 " pdb=" CB LEU K 4 " pdb=" CG LEU K 4 " pdb=" CD1 LEU K 4 " ideal model delta sinusoidal sigma weight residual 180.00 144.10 35.90 3 1.50e+01 4.44e-03 6.18e+00 ... (remaining 549 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.038: 120 0.038 - 0.075: 48 0.075 - 0.112: 16 0.112 - 0.149: 0 0.149 - 0.185: 8 Chirality restraints: 192 Sorted by residual: chirality pdb=" CG LEU R 4 " pdb=" CB LEU R 4 " pdb=" CD1 LEU R 4 " pdb=" CD2 LEU R 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CG LEU I 4 " pdb=" CB LEU I 4 " pdb=" CD1 LEU I 4 " pdb=" CD2 LEU I 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CG LEU L 4 " pdb=" CB LEU L 4 " pdb=" CD1 LEU L 4 " pdb=" CD2 LEU L 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.47e-01 ... (remaining 189 not shown) Planarity restraints: 136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 4 " -0.002 2.00e-02 2.50e+03 3.39e-03 1.15e-01 pdb=" C LEU I 4 " 0.006 2.00e-02 2.50e+03 pdb=" O LEU I 4 " -0.002 2.00e-02 2.50e+03 pdb=" N LEU I 5 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 4 " 0.002 2.00e-02 2.50e+03 3.39e-03 1.15e-01 pdb=" C LEU R 4 " -0.006 2.00e-02 2.50e+03 pdb=" O LEU R 4 " 0.002 2.00e-02 2.50e+03 pdb=" N LEU R 5 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU X 4 " 0.002 2.00e-02 2.50e+03 3.34e-03 1.12e-01 pdb=" C LEU X 4 " -0.006 2.00e-02 2.50e+03 pdb=" O LEU X 4 " 0.002 2.00e-02 2.50e+03 pdb=" N LEU X 5 " 0.002 2.00e-02 2.50e+03 ... (remaining 133 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 48 2.72 - 3.26: 1116 3.26 - 3.81: 2110 3.81 - 4.35: 2730 4.35 - 4.90: 4930 Nonbonded interactions: 10934 Sorted by model distance: nonbonded pdb=" O58 UQ4 I 1 " pdb=" O58 UQ4 R 1 " model vdw 2.169 3.040 nonbonded pdb=" O58 UQ4 C 1 " pdb=" O58 UQ4 U 1 " model vdw 2.170 3.040 nonbonded pdb=" O58 UQ4 F 1 " pdb=" O58 UQ4 O 1 " model vdw 2.170 3.040 nonbonded pdb=" O58 UQ4 L 1 " pdb=" O58 UQ4 X 1 " model vdw 2.170 3.040 nonbonded pdb=" N52 UQ4 M 1 " pdb=" O01 UQ4 M 1 " model vdw 2.420 3.120 ... (remaining 10929 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.000 Extract box with map and model: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.050 0.169 1344 Z= 2.763 Angle : 2.197 8.924 1752 Z= 0.752 Chirality : 0.056 0.185 192 Planarity : 0.001 0.003 136 Dihedral : 26.689 72.701 360 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 29.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -9.60 (0.20), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.31 (0.15), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.04854 / 2.42 ( 1320) covalent geometry : angle 2.19652 / 0.75 ( 1752) Misc. bond : bond 0.10220 / 5.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0129 time to fit residues: 0.5616 Evaluate side-chains 5 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.062400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.059476 restraints weight = 7482.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.060602 restraints weight = 2560.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061363 restraints weight = 1183.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.061629 restraints weight = 618.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.061916 restraints weight = 417.989| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1344 Z= 0.173 Angle : 0.886 8.134 1752 Z= 0.300 Chirality : 0.036 0.142 192 Planarity : 0.001 0.005 136 Dihedral : 20.165 58.814 168 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 11.46 % Allowed : 28.12 % Favored : 60.42 % 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: -9.32 (0.26), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.10 (0.20), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 1320) covalent geometry : angle 0.88598 / 0.30 ( 1752) Misc. bond : bond 0.00113 / 0.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 8 time to evaluate : 0.030 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 18 average time/residue: 0.0125 time to fit residues: 0.3113 Evaluate side-chains 8 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 4 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain W residue 2 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.055628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.053648 restraints weight = 8421.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.054372 restraints weight = 2558.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.054788 restraints weight = 1173.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.054953 restraints weight = 659.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.055110 restraints weight = 407.741| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.052 1344 Z= 0.708 Angle : 1.546 13.843 1752 Z= 0.544 Chirality : 0.056 0.214 192 Planarity : 0.003 0.006 136 Dihedral : 22.745 58.253 168 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.92 % Favored : 77.08 % Rotamer: Outliers : 12.50 % Allowed : 40.62 % Favored : 46.88 % 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: -8.65 (0.44), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.59 (0.34), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.01594 / 0.71 ( 1320) covalent geometry : angle 1.54553 / 0.54 ( 1752) Misc. bond : bond 0.00318 / 0.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 2 time to evaluate : 0.021 Fit side-chains REVERT: B 2 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.8874 (mm) outliers start: 12 outliers final: 10 residues processed: 14 average time/residue: 0.0120 time to fit residues: 0.2418 Evaluate side-chains 13 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 2 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 2 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.060729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.058861 restraints weight = 7902.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.059546 restraints weight = 2103.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.060042 restraints weight = 908.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.060193 restraints weight = 479.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.060356 restraints weight = 294.253| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1344 Z= 0.096 Angle : 0.774 9.948 1752 Z= 0.264 Chirality : 0.029 0.116 192 Planarity : 0.001 0.005 136 Dihedral : 18.688 58.986 168 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 6.25 % Allowed : 46.88 % Favored : 46.88 % 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: -8.02 (0.53), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.11 (0.41), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 1320) covalent geometry : angle 0.77413 / 0.26 ( 1752) Misc. bond : bond 0.00057 / 0.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.022 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 14 average time/residue: 0.0128 time to fit residues: 0.2542 Evaluate side-chains 11 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.058439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.056759 restraints weight = 8263.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.057375 restraints weight = 2399.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.057706 restraints weight = 1038.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.057930 restraints weight = 557.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.057982 restraints weight = 333.509| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.051 1344 Z= 0.705 Angle : 1.548 14.532 1752 Z= 0.548 Chirality : 0.049 0.182 192 Planarity : 0.003 0.007 136 Dihedral : 23.895 59.864 168 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 11.46 % Allowed : 45.83 % Favored : 42.71 % 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: -8.32 (0.52), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.33 (0.40), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.01609 / 0.71 ( 1320) covalent geometry : angle 1.54833 / 0.55 ( 1752) Misc. bond : bond 0.00310 / 0.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 4 time to evaluate : 0.021 Fit side-chains REVERT: B 2 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.8968 (mm) outliers start: 11 outliers final: 8 residues processed: 15 average time/residue: 0.0127 time to fit residues: 0.2698 Evaluate side-chains 13 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 4 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.061036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.059078 restraints weight = 7995.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.059788 restraints weight = 2233.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.060194 restraints weight = 960.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.060550 restraints weight = 555.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.060672 restraints weight = 330.411| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1344 Z= 0.098 Angle : 0.800 10.038 1752 Z= 0.271 Chirality : 0.026 0.096 192 Planarity : 0.001 0.005 136 Dihedral : 18.377 58.172 168 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.33 % Allowed : 47.92 % Favored : 43.75 % 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: -7.75 (0.56), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.90 (0.43), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 1320) covalent geometry : angle 0.79960 / 0.27 ( 1752) Misc. bond : bond 0.00056 / 0.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 8 time to evaluate : 0.022 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 16 average time/residue: 0.0167 time to fit residues: 0.3586 Evaluate side-chains 11 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.056887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.054807 restraints weight = 8282.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.055447 restraints weight = 2398.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.055938 restraints weight = 1119.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.056175 restraints weight = 650.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.056374 restraints weight = 407.839| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.6318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.049 1344 Z= 0.697 Angle : 1.549 12.728 1752 Z= 0.549 Chirality : 0.047 0.169 192 Planarity : 0.003 0.007 136 Dihedral : 24.076 73.816 168 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 12.50 % Allowed : 42.71 % Favored : 44.79 % 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: -7.83 (0.62), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.47), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.01593 / 0.70 ( 1320) covalent geometry : angle 1.54896 / 0.55 ( 1752) Misc. bond : bond 0.00313 / 0.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 4 time to evaluate : 0.022 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 16 average time/residue: 0.0174 time to fit residues: 0.3864 Evaluate side-chains 11 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 4 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.060248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.058315 restraints weight = 7907.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.058974 restraints weight = 2174.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.059380 restraints weight = 913.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.059748 restraints weight = 512.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.059922 restraints weight = 290.560| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1344 Z= 0.098 Angle : 0.827 8.339 1752 Z= 0.277 Chirality : 0.025 0.095 192 Planarity : 0.001 0.005 136 Dihedral : 16.779 54.451 168 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 8.33 % Allowed : 43.75 % Favored : 47.92 % 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: -7.40 (0.65), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.64 (0.50), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 1320) covalent geometry : angle 0.82676 / 0.28 ( 1752) Misc. bond : bond 0.00052 / 0.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.023 Fit side-chains REVERT: H 2 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8370 (pp) outliers start: 8 outliers final: 5 residues processed: 16 average time/residue: 0.0135 time to fit residues: 0.3020 Evaluate side-chains 12 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 6 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.057067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.054943 restraints weight = 8429.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.055637 restraints weight = 2496.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.056056 restraints weight = 1143.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.056331 restraints weight = 696.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.056449 restraints weight = 439.612| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.046 1344 Z= 0.692 Angle : 1.522 11.125 1752 Z= 0.542 Chirality : 0.046 0.160 192 Planarity : 0.003 0.007 136 Dihedral : 23.912 79.044 168 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.92 % Favored : 77.08 % Rotamer: Outliers : 9.38 % Allowed : 45.83 % Favored : 44.79 % 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: -7.78 (0.63), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.92 (0.48), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.01583 / 0.70 ( 1320) covalent geometry : angle 1.52168 / 0.54 ( 1752) Misc. bond : bond 0.00305 / 0.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 4 time to evaluate : 0.023 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 13 average time/residue: 0.0119 time to fit residues: 0.2283 Evaluate side-chains 10 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 4 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.060129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.058239 restraints weight = 7814.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.058860 restraints weight = 2117.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.059373 restraints weight = 898.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.059626 restraints weight = 476.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.059681 restraints weight = 267.169| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1344 Z= 0.092 Angle : 0.845 7.714 1752 Z= 0.282 Chirality : 0.025 0.091 192 Planarity : 0.001 0.005 136 Dihedral : 16.618 54.693 168 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.21 % Allowed : 48.96 % Favored : 45.83 % 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: -7.21 (0.69), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.49 (0.53), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 ( 1320) covalent geometry : angle 0.84451 / 0.28 ( 1752) Misc. bond : bond 0.00043 / 0.02 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 9 time to evaluate : 0.023 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 13 average time/residue: 0.0137 time to fit residues: 0.2558 Evaluate side-chains 11 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.058699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.056626 restraints weight = 8331.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.057358 restraints weight = 2537.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.057890 restraints weight = 1167.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.058127 restraints weight = 646.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.058312 restraints weight = 396.202| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.053 1344 Z= 0.697 Angle : 1.507 10.989 1752 Z= 0.541 Chirality : 0.046 0.160 192 Planarity : 0.003 0.007 136 Dihedral : 24.079 79.260 168 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % Rotamer: Outliers : 6.25 % Allowed : 46.88 % Favored : 46.88 % 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: -7.87 (0.60), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.99 (0.45), residues: 48 Details of bonding type rmsd/Z covalent geometry : bond 0.01593 / 0.70 ( 1320) covalent geometry : angle 1.50699 / 0.54 ( 1752) Misc. bond : bond 0.00313 / 0.16 ( 24) =============================================================================== Job complete usr+sys time: 148.52 seconds wall clock time: 3 minutes 31.65 seconds (211.65 seconds total)