Starting phenix.real_space_refine on Thu Oct 22 20:53:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cz3_46060/10_2026/9cz3_46060_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cz3_46060/10_2026/9cz3_46060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cz3_46060/10_2026/9cz3_46060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cz3_46060/10_2026/9cz3_46060.map" model { file = "/net/cci-nas-00/data/ceres_data/9cz3_46060/10_2026/9cz3_46060_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cz3_46060/10_2026/9cz3_46060_trim.cif" } resolution = 2.7 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= 0.094 sd= 0.655 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: 4 Type Number sf(0) Gaussians C 1710 2.51 5 N 405 2.21 5 O 315 1.98 5 H 3150 0.53 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: 5580 Number of models: 1 Model: "" Number of chains: 90 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.12, per 1000 atoms: 0.20 Number of scatterers: 5580 At special positions: 0 Unit cell: (97.2, 97.2, 34.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 315 8.00 N 405 7.00 C 1710 6.00 H 3150 1.00 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=45, symmetry=0 Number of additional bonds: simple=45, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 81.9 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 5.634A pdb=" N ILE A 2 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU D 5 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A 4 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE D 2 " --> pdb=" O ILE G 3 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU G 5 " --> pdb=" O ILE D 2 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE D 4 " --> pdb=" O LEU G 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.657A pdb=" N ILE E 3 " --> pdb=" O ILE B 2 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE H 3 " --> pdb=" O ILE E 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 removed outlier: 3.528A pdb=" N ILE F 4 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 2 through 5 removed outlier: 5.519A pdb=" N ILE J 2 " --> pdb=" O ILE M 3 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU M 5 " --> pdb=" O ILE J 2 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE J 4 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE M 2 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU P 5 " --> pdb=" O ILE M 2 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE M 4 " --> pdb=" O LEU P 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 2 through 5 removed outlier: 3.544A pdb=" N ILE N 3 " --> pdb=" O ILE K 2 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE Q 3 " --> pdb=" O ILE N 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU Q 5 " --> pdb=" O ILE N 4 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'S' and resid 2 through 5 removed outlier: 5.727A pdb=" N ILE S 2 " --> pdb=" O ILE V 3 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU V 5 " --> pdb=" O ILE S 2 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE S 4 " --> pdb=" O LEU V 5 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE V 2 " --> pdb=" O ILE Y 3 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU Y 5 " --> pdb=" O ILE V 2 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE V 4 " --> pdb=" O LEU Y 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'T' and resid 2 through 3 removed outlier: 7.391A pdb=" N ILE T 2 " --> pdb=" O ILE W 3 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N LEU W 5 " --> pdb=" O ILE T 2 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE Z 3 " --> pdb=" O ILE W 2 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU Z 5 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 2 through 4 removed outlier: 3.838A pdb=" N ILE X 4 " --> pdb=" O ILE U 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 2 through 5 removed outlier: 6.083A pdb=" N ILE b 2 " --> pdb=" O ILE e 3 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU e 5 " --> pdb=" O ILE b 2 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE b 4 " --> pdb=" O LEU e 5 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE e 2 " --> pdb=" O ILE h 3 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU h 5 " --> pdb=" O ILE e 2 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE e 4 " --> pdb=" O LEU h 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'c' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'd' and resid 2 through 4 Processing sheet with id=AB4, first strand: chain 'k' and resid 2 through 5 removed outlier: 5.634A pdb=" N ILE k 2 " --> pdb=" O ILE n 3 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU n 5 " --> pdb=" O ILE k 2 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE k 4 " --> pdb=" O LEU n 5 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE n 2 " --> pdb=" O ILE q 3 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU q 5 " --> pdb=" O ILE n 2 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE n 4 " --> pdb=" O LEU q 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'l' and resid 2 through 5 removed outlier: 3.592A pdb=" N ILE o 3 " --> pdb=" O ILE l 2 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU r 5 " --> pdb=" O ILE o 4 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 2 through 4 37 hydrogen bonds defined for protein. 111 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: 0.84 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.11: 3150 1.11 - 1.23: 250 1.23 - 1.35: 335 1.35 - 1.47: 145 1.47 - 1.59: 1610 Bond restraints: 5490 Sorted by residual: bond pdb=" N LYS O 1 " pdb=" H LYS O 1 " ideal model delta sigma weight residual 0.860 1.002 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N LYS d 1 " pdb=" H LYS d 1 " ideal model delta sigma weight residual 0.860 1.002 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N LYS U 1 " pdb=" H LYS U 1 " ideal model delta sigma weight residual 0.860 1.001 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" N LYS F 1 " pdb=" H LYS F 1 " ideal model delta sigma weight residual 0.860 1.001 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" N LYS p 1 " pdb=" H LYS p 1 " ideal model delta sigma weight residual 0.860 1.001 -0.141 2.00e-02 2.50e+03 4.98e+01 ... (remaining 5485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 8908 2.08 - 4.17: 900 4.17 - 6.25: 443 6.25 - 8.33: 38 8.33 - 10.42: 16 Bond angle restraints: 10305 Sorted by residual: angle pdb=" CA ILE S 3 " pdb=" CB ILE S 3 " pdb=" CG1 ILE S 3 " ideal model delta sigma weight residual 110.40 117.61 -7.21 1.70e+00 3.46e-01 1.80e+01 angle pdb=" CA ILE n 3 " pdb=" CB ILE n 3 " pdb=" CG1 ILE n 3 " ideal model delta sigma weight residual 110.40 117.50 -7.10 1.70e+00 3.46e-01 1.74e+01 angle pdb=" C LEU f 5 " pdb=" CA LEU f 5 " pdb=" CB LEU f 5 " ideal model delta sigma weight residual 109.65 116.70 -7.05 1.75e+00 3.27e-01 1.62e+01 angle pdb=" CA ILE D 3 " pdb=" CB ILE D 3 " pdb=" CG1 ILE D 3 " ideal model delta sigma weight residual 110.40 117.16 -6.76 1.70e+00 3.46e-01 1.58e+01 angle pdb=" C LEU N 5 " pdb=" CA LEU N 5 " pdb=" CB LEU N 5 " ideal model delta sigma weight residual 109.65 116.02 -6.37 1.75e+00 3.27e-01 1.33e+01 ... (remaining 10300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 2235 36.00 - 72.00: 44 72.00 - 108.00: 0 108.00 - 144.00: 0 144.00 - 179.99: 16 Dihedral angle restraints: 2295 sinusoidal: 1530 harmonic: 765 Sorted by residual: dihedral pdb=" CH3 ACE J 0 " pdb=" C ACE J 0 " pdb=" N LYS J 1 " pdb=" CA LYS J 1 " ideal model delta sinusoidal sigma weight residual 180.00 0.01 179.99 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE T 0 " pdb=" C ACE T 0 " pdb=" N LYS T 1 " pdb=" CA LYS T 1 " ideal model delta sinusoidal sigma weight residual -180.00 -2.22 -177.78 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE G 0 " pdb=" C ACE G 0 " pdb=" N LYS G 1 " pdb=" CA LYS G 1 " ideal model delta sinusoidal sigma weight residual 180.00 3.52 176.48 1 5.00e+00 4.00e-02 7.67e+02 ... (remaining 2292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 172 0.067 - 0.134: 137 0.134 - 0.200: 122 0.200 - 0.267: 18 0.267 - 0.334: 1 Chirality restraints: 450 Sorted by residual: chirality pdb=" CA LYS G 1 " pdb=" N LYS G 1 " pdb=" C LYS G 1 " pdb=" CB LYS G 1 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ILE F 2 " pdb=" N ILE F 2 " pdb=" C ILE F 2 " pdb=" CB ILE F 2 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ILE o 2 " pdb=" N ILE o 2 " pdb=" C ILE o 2 " pdb=" CB ILE o 2 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 447 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE Z 0 " 0.172 2.00e-02 2.50e+03 9.42e-02 1.33e+02 pdb=" O ACE Z 0 " -0.018 2.00e-02 2.50e+03 pdb=" CH3 ACE Z 0 " -0.103 2.00e-02 2.50e+03 pdb=" N LYS Z 1 " 0.026 2.00e-02 2.50e+03 pdb=" CA LYS Z 1 " 0.029 2.00e-02 2.50e+03 pdb=" H LYS Z 1 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE k 0 " 0.136 2.00e-02 2.50e+03 9.41e-02 1.33e+02 pdb=" O ACE k 0 " -0.143 2.00e-02 2.50e+03 pdb=" CH3 ACE k 0 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS k 1 " 0.036 2.00e-02 2.50e+03 pdb=" CA LYS k 1 " -0.099 2.00e-02 2.50e+03 pdb=" H LYS k 1 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE V 0 " -0.149 2.00e-02 2.50e+03 8.88e-02 1.18e+02 pdb=" O ACE V 0 " 0.128 2.00e-02 2.50e+03 pdb=" CH3 ACE V 0 " 0.001 2.00e-02 2.50e+03 pdb=" N LYS V 1 " -0.036 2.00e-02 2.50e+03 pdb=" CA LYS V 1 " 0.082 2.00e-02 2.50e+03 pdb=" H LYS V 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.31: 751 2.31 - 2.83: 11689 2.83 - 3.35: 11630 3.35 - 3.88: 15294 3.88 - 4.40: 21469 Nonbonded interactions: 60833 Sorted by model distance: nonbonded pdb=" O ACE G 0 " pdb=" HZ1 LYS I 6 " model vdw 1.782 2.450 nonbonded pdb=" O ACE Y 0 " pdb=" HZ1 LYS a 6 " model vdw 1.810 2.450 nonbonded pdb=" O ACE V 0 " pdb=" HZ1 LYS X 6 " model vdw 1.829 2.450 nonbonded pdb=" O ACE e 0 " pdb=" HZ1 LYS g 6 " model vdw 1.839 2.450 nonbonded pdb=" O ACE h 0 " pdb=" HZ1 LYS j 6 " model vdw 1.840 2.450 ... (remaining 60828 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 '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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = 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' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.150 Find NCS groups from input model: 0.110 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.020 0.111 2385 Z= 1.571 Angle : 1.858 10.417 3015 Z= 0.988 Chirality : 0.115 0.334 450 Planarity : 0.017 0.097 270 Dihedral : 25.026 179.994 1035 Min Nonbonded Distance : 2.701 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.57), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.90 (0.43), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.01406 / 0.71 ( 2340) covalent geometry : angle 1.85807 / 0.99 ( 3015) hydrogen bonds : bond 0.32649 / 20.27 ( 37) hydrogen bonds : angle 12.79465 / 7.75 ( 111) Misc. bond : bond 0.10222 / 6.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8921 (pttt) cc_final: 0.8645 (mptt) REVERT: H 6 LYS cc_start: 0.9108 (mptt) cc_final: 0.8601 (pmtt) REVERT: I 6 LYS cc_start: 0.7423 (pttt) cc_final: 0.7023 (tppt) REVERT: J 1 LYS cc_start: 0.8393 (mttm) cc_final: 0.7985 (mmmt) REVERT: J 6 LYS cc_start: 0.8886 (mttt) cc_final: 0.8215 (mmpt) REVERT: O 6 LYS cc_start: 0.7880 (tttt) cc_final: 0.7594 (mtpt) REVERT: P 1 LYS cc_start: 0.8462 (mttm) cc_final: 0.8131 (mtmt) REVERT: Q 6 LYS cc_start: 0.9037 (tttt) cc_final: 0.8755 (pmtt) REVERT: R 6 LYS cc_start: 0.7560 (tttt) cc_final: 0.6927 (mmpt) REVERT: S 1 LYS cc_start: 0.8191 (mttm) cc_final: 0.7719 (mmmt) REVERT: S 6 LYS cc_start: 0.9030 (mttt) cc_final: 0.8515 (mmtt) REVERT: U 6 LYS cc_start: 0.7599 (tttt) cc_final: 0.6660 (pttt) REVERT: Y 1 LYS cc_start: 0.8394 (mttm) cc_final: 0.8159 (mtmt) REVERT: a 6 LYS cc_start: 0.7842 (tttt) cc_final: 0.6989 (mmpt) REVERT: b 1 LYS cc_start: 0.8275 (mttm) cc_final: 0.7582 (mmpt) REVERT: c 6 LYS cc_start: 0.9087 (pttt) cc_final: 0.8472 (mmtm) REVERT: g 6 LYS cc_start: 0.7547 (tttt) cc_final: 0.7112 (mtpp) REVERT: i 6 LYS cc_start: 0.8841 (mptt) cc_final: 0.8423 (pmtt) REVERT: j 6 LYS cc_start: 0.7343 (tttt) cc_final: 0.6514 (mmpt) REVERT: k 1 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7795 (tptt) REVERT: p 6 LYS cc_start: 0.7484 (tttt) cc_final: 0.7052 (mtpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 1.9419 time to fit residues: 153.4452 Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.079538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.075711 restraints weight = 43229.463| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 4.10 r_work: 0.4087 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2385 Z= 0.137 Angle : 0.702 4.889 3015 Z= 0.340 Chirality : 0.066 0.173 450 Planarity : 0.002 0.010 270 Dihedral : 41.756 179.958 315 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.59 % Allowed : 18.89 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.62), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.70 (0.47), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 2340) covalent geometry : angle 0.70248 / 0.34 ( 3015) hydrogen bonds : bond 0.08460 / 5.32 ( 37) hydrogen bonds : angle 9.18432 / 5.76 ( 111) Misc. bond : bond 0.00032 / 0.02 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 LYS cc_start: 0.8264 (mttm) cc_final: 0.7964 (mmmt) REVERT: J 6 LYS cc_start: 0.8776 (mttt) cc_final: 0.8177 (mmpt) REVERT: R 6 LYS cc_start: 0.7003 (tttt) cc_final: 0.6620 (mmpt) REVERT: S 1 LYS cc_start: 0.8035 (mttm) cc_final: 0.7584 (mmmt) REVERT: S 6 LYS cc_start: 0.8746 (mttt) cc_final: 0.8404 (mmpt) REVERT: T 6 LYS cc_start: 0.8866 (pttt) cc_final: 0.8079 (tppt) REVERT: U 6 LYS cc_start: 0.7121 (tttt) cc_final: 0.6443 (pttt) REVERT: Y 1 LYS cc_start: 0.8267 (mttm) cc_final: 0.7688 (mptt) REVERT: a 6 LYS cc_start: 0.7496 (tttt) cc_final: 0.6838 (mmpt) REVERT: b 1 LYS cc_start: 0.8047 (mttm) cc_final: 0.7377 (mmmt) REVERT: j 6 LYS cc_start: 0.7075 (tttt) cc_final: 0.6350 (mmpt) outliers start: 7 outliers final: 2 residues processed: 42 average time/residue: 2.1277 time to fit residues: 90.6444 Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain f residue 6 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.080202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.077288 restraints weight = 46942.501| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 3.67 r_work: 0.4060 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.8400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 2385 Z= 0.313 Angle : 0.798 4.884 3015 Z= 0.386 Chirality : 0.064 0.158 450 Planarity : 0.003 0.013 270 Dihedral : 41.671 179.998 315 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.44 % Allowed : 24.44 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.66), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.67 (0.50), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.32 ( 2340) covalent geometry : angle 0.79849 / 0.39 ( 3015) hydrogen bonds : bond 0.10563 / 6.70 ( 37) hydrogen bonds : angle 9.59242 / 5.87 ( 111) Misc. bond : bond 0.00095 / 0.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7934 (tttt) cc_final: 0.6946 (pttt) REVERT: J 1 LYS cc_start: 0.8393 (mttm) cc_final: 0.8105 (mmmt) REVERT: J 6 LYS cc_start: 0.9254 (mttt) cc_final: 0.8367 (mmpt) REVERT: R 6 LYS cc_start: 0.7475 (tttt) cc_final: 0.6662 (mmpt) REVERT: S 6 LYS cc_start: 0.9132 (mttt) cc_final: 0.8400 (mmpt) REVERT: T 6 LYS cc_start: 0.9179 (pttt) cc_final: 0.8404 (tptt) REVERT: U 1 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5906 (mmtp) REVERT: U 6 LYS cc_start: 0.7032 (tttt) cc_final: 0.6108 (pttt) REVERT: j 6 LYS cc_start: 0.7558 (tttt) cc_final: 0.6263 (mmpt) REVERT: l 6 LYS cc_start: 0.5432 (OUTLIER) cc_final: 0.4943 (mptt) REVERT: m 6 LYS cc_start: 0.7515 (tttt) cc_final: 0.7102 (pttt) REVERT: s 1 LYS cc_start: 0.5842 (OUTLIER) cc_final: 0.4163 (pmtt) outliers start: 12 outliers final: 1 residues processed: 29 average time/residue: 1.8183 time to fit residues: 53.6655 Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.079338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.076223 restraints weight = 48296.535| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.96 r_work: 0.4024 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.8921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2385 Z= 0.253 Angle : 0.710 4.981 3015 Z= 0.342 Chirality : 0.064 0.163 450 Planarity : 0.002 0.008 270 Dihedral : 41.569 179.897 315 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.33 % Allowed : 28.15 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.67), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.65 (0.51), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.26 ( 2340) covalent geometry : angle 0.70971 / 0.34 ( 3015) hydrogen bonds : bond 0.09010 / 5.83 ( 37) hydrogen bonds : angle 8.90335 / 5.47 ( 111) Misc. bond : bond 0.00081 / 0.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 15 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 LYS cc_start: 0.8335 (mttm) cc_final: 0.8107 (mmmt) REVERT: J 6 LYS cc_start: 0.9175 (mttt) cc_final: 0.8450 (mmpt) REVERT: S 6 LYS cc_start: 0.9174 (mttt) cc_final: 0.8250 (mmpt) REVERT: U 6 LYS cc_start: 0.6893 (tttt) cc_final: 0.5938 (pttt) REVERT: a 6 LYS cc_start: 0.8017 (tttt) cc_final: 0.6818 (mmpt) REVERT: d 6 LYS cc_start: 0.6931 (tttt) cc_final: 0.5954 (pttt) REVERT: j 6 LYS cc_start: 0.7730 (tttt) cc_final: 0.6206 (mmpt) REVERT: m 6 LYS cc_start: 0.7578 (tttt) cc_final: 0.7136 (pttt) REVERT: s 6 LYS cc_start: 0.4452 (OUTLIER) cc_final: 0.4215 (mmtt) outliers start: 9 outliers final: 1 residues processed: 23 average time/residue: 1.9112 time to fit residues: 44.8340 Evaluate side-chains 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain s residue 6 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.079010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.076109 restraints weight = 48676.657| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.58 r_work: 0.4046 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.9153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 2385 Z= 0.314 Angle : 0.757 5.087 3015 Z= 0.364 Chirality : 0.063 0.156 450 Planarity : 0.002 0.009 270 Dihedral : 41.661 179.951 315 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.96 % Allowed : 29.63 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.68), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.49 (0.52), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.32 ( 2340) covalent geometry : angle 0.75668 / 0.36 ( 3015) hydrogen bonds : bond 0.09790 / 6.34 ( 37) hydrogen bonds : angle 9.27594 / 5.69 ( 111) Misc. bond : bond 0.00133 / 0.09 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 12 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6224 (mmtm) REVERT: J 6 LYS cc_start: 0.9103 (mttt) cc_final: 0.8554 (mmpt) REVERT: S 6 LYS cc_start: 0.9067 (mttt) cc_final: 0.8303 (mmpt) REVERT: T 6 LYS cc_start: 0.9166 (pttt) cc_final: 0.8402 (tptt) REVERT: U 6 LYS cc_start: 0.6747 (tttt) cc_final: 0.5836 (pttt) REVERT: d 6 LYS cc_start: 0.7000 (tttt) cc_final: 0.5943 (pttt) REVERT: j 6 LYS cc_start: 0.7723 (tttt) cc_final: 0.6245 (mmpt) REVERT: m 6 LYS cc_start: 0.7565 (tttt) cc_final: 0.7244 (pttt) outliers start: 8 outliers final: 3 residues processed: 20 average time/residue: 1.8146 time to fit residues: 37.0625 Evaluate side-chains 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.079187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.076335 restraints weight = 49160.646| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.56 r_work: 0.4039 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.9405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2385 Z= 0.258 Angle : 0.712 5.179 3015 Z= 0.343 Chirality : 0.064 0.155 450 Planarity : 0.002 0.009 270 Dihedral : 41.607 179.884 315 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.44 % Allowed : 29.26 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.67), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.39 (0.51), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.26 ( 2340) covalent geometry : angle 0.71213 / 0.34 ( 3015) hydrogen bonds : bond 0.08927 / 5.81 ( 37) hydrogen bonds : angle 8.90854 / 5.47 ( 111) Misc. bond : bond 0.00080 / 0.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 12 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6201 (mmtm) REVERT: J 6 LYS cc_start: 0.9123 (mttt) cc_final: 0.8583 (mmpt) REVERT: S 6 LYS cc_start: 0.9105 (mttt) cc_final: 0.8399 (mmpt) REVERT: T 6 LYS cc_start: 0.9153 (pttt) cc_final: 0.8328 (tptt) REVERT: U 6 LYS cc_start: 0.6916 (tttt) cc_final: 0.5975 (pttt) REVERT: d 6 LYS cc_start: 0.7051 (tttt) cc_final: 0.5947 (pttt) REVERT: j 6 LYS cc_start: 0.7867 (tttt) cc_final: 0.6328 (mmpt) REVERT: m 6 LYS cc_start: 0.7705 (tttt) cc_final: 0.7293 (pttt) REVERT: s 1 LYS cc_start: 0.5796 (OUTLIER) cc_final: 0.5373 (pptt) outliers start: 12 outliers final: 5 residues processed: 24 average time/residue: 1.8207 time to fit residues: 44.5164 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.078937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.076319 restraints weight = 49612.581| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 3.19 r_work: 0.4067 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.9588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 2385 Z= 0.310 Angle : 0.763 5.656 3015 Z= 0.367 Chirality : 0.063 0.156 450 Planarity : 0.002 0.008 270 Dihedral : 41.662 179.945 315 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.81 % Allowed : 29.63 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.67), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.40 (0.51), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.31 ( 2340) covalent geometry : angle 0.76336 / 0.37 ( 3015) hydrogen bonds : bond 0.09583 / 6.18 ( 37) hydrogen bonds : angle 9.16760 / 5.62 ( 111) Misc. bond : bond 0.00100 / 0.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 11 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: C 1 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6229 (mmtm) REVERT: S 6 LYS cc_start: 0.9040 (mttt) cc_final: 0.8421 (mmpt) REVERT: T 6 LYS cc_start: 0.9124 (pttt) cc_final: 0.8326 (tptt) REVERT: U 6 LYS cc_start: 0.6920 (tttt) cc_final: 0.5991 (pttt) REVERT: d 6 LYS cc_start: 0.7009 (tttt) cc_final: 0.5945 (pttt) REVERT: j 6 LYS cc_start: 0.7829 (tttt) cc_final: 0.6299 (mmpt) REVERT: m 6 LYS cc_start: 0.7473 (tttt) cc_final: 0.7061 (pttt) REVERT: s 1 LYS cc_start: 0.5934 (OUTLIER) cc_final: 0.5526 (pptt) outliers start: 13 outliers final: 4 residues processed: 24 average time/residue: 1.6523 time to fit residues: 40.5212 Evaluate side-chains 15 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain a residue 1 LYS Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.079882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.077222 restraints weight = 48701.740| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.30 r_work: 0.4075 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.9740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2385 Z= 0.257 Angle : 0.723 5.411 3015 Z= 0.346 Chirality : 0.064 0.154 450 Planarity : 0.002 0.009 270 Dihedral : 41.675 179.993 315 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.96 % Allowed : 31.48 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.68), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.35 (0.52), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.26 ( 2340) covalent geometry : angle 0.72329 / 0.35 ( 3015) hydrogen bonds : bond 0.08899 / 5.70 ( 37) hydrogen bonds : angle 8.86599 / 5.43 ( 111) Misc. bond : bond 0.00079 / 0.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 7 time to evaluate : 0.144 Fit side-chains REVERT: C 1 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6273 (mmtm) REVERT: C 6 LYS cc_start: 0.7368 (ttpp) cc_final: 0.6113 (pttt) REVERT: S 6 LYS cc_start: 0.9079 (mttt) cc_final: 0.8462 (mmpt) REVERT: U 6 LYS cc_start: 0.6995 (tttt) cc_final: 0.5997 (pttt) REVERT: a 1 LYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5057 (pmtt) REVERT: d 6 LYS cc_start: 0.6965 (tttt) cc_final: 0.5892 (pttt) REVERT: j 6 LYS cc_start: 0.7844 (tttt) cc_final: 0.6299 (mmpt) REVERT: m 6 LYS cc_start: 0.7497 (tttt) cc_final: 0.7025 (pttt) REVERT: s 1 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5617 (pptt) outliers start: 8 outliers final: 3 residues processed: 15 average time/residue: 1.8495 time to fit residues: 28.3681 Evaluate side-chains 13 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 7 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain a residue 1 LYS Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.079669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.076978 restraints weight = 49095.437| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.41 r_work: 0.4060 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.9799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2385 Z= 0.262 Angle : 0.721 5.218 3015 Z= 0.345 Chirality : 0.063 0.156 450 Planarity : 0.002 0.009 270 Dihedral : 41.712 179.853 315 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.22 % Allowed : 31.85 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.69), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.38 (0.52), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.26 ( 2340) covalent geometry : angle 0.72054 / 0.35 ( 3015) hydrogen bonds : bond 0.08896 / 5.71 ( 37) hydrogen bonds : angle 8.86196 / 5.39 ( 111) Misc. bond : bond 0.00081 / 0.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.176 Fit side-chains REVERT: C 1 LYS cc_start: 0.6363 (OUTLIER) cc_final: 0.6083 (mmtm) REVERT: C 6 LYS cc_start: 0.7532 (ttpp) cc_final: 0.6237 (pttt) REVERT: S 6 LYS cc_start: 0.9159 (mttt) cc_final: 0.8395 (mmtt) REVERT: U 6 LYS cc_start: 0.7106 (tttt) cc_final: 0.6066 (pttt) REVERT: d 6 LYS cc_start: 0.7059 (tttt) cc_final: 0.5914 (pttt) REVERT: j 6 LYS cc_start: 0.7884 (tttt) cc_final: 0.6243 (mmpt) REVERT: m 6 LYS cc_start: 0.7592 (tttt) cc_final: 0.7008 (pttt) REVERT: s 1 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5432 (pptt) outliers start: 6 outliers final: 3 residues processed: 14 average time/residue: 1.7326 time to fit residues: 24.8457 Evaluate side-chains 13 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 8 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.079762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.077050 restraints weight = 48990.741| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.37 r_work: 0.4064 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.9835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2385 Z= 0.257 Angle : 0.716 5.207 3015 Z= 0.343 Chirality : 0.064 0.155 450 Planarity : 0.002 0.008 270 Dihedral : 41.721 179.879 315 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.85 % Allowed : 32.22 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.69), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.41 (0.53), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.26 ( 2340) covalent geometry : angle 0.71589 / 0.34 ( 3015) hydrogen bonds : bond 0.08858 / 5.69 ( 37) hydrogen bonds : angle 8.84422 / 5.38 ( 111) Misc. bond : bond 0.00080 / 0.05 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6206 (mmtm) REVERT: C 6 LYS cc_start: 0.7487 (ttpp) cc_final: 0.6234 (pttt) REVERT: S 6 LYS cc_start: 0.9071 (mttt) cc_final: 0.8403 (mmtt) REVERT: U 6 LYS cc_start: 0.6999 (tttt) cc_final: 0.6006 (pttt) REVERT: d 6 LYS cc_start: 0.6985 (tttt) cc_final: 0.5884 (pttt) REVERT: j 6 LYS cc_start: 0.7890 (tttt) cc_final: 0.6329 (mmpt) REVERT: m 6 LYS cc_start: 0.7541 (tttt) cc_final: 0.6983 (pttt) REVERT: s 1 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5555 (pptt) outliers start: 5 outliers final: 2 residues processed: 15 average time/residue: 1.7301 time to fit residues: 26.5845 Evaluate side-chains 12 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 8 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.078656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.075826 restraints weight = 49361.610| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.55 r_work: 0.4016 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.9867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 2385 Z= 0.306 Angle : 0.768 5.283 3015 Z= 0.368 Chirality : 0.064 0.158 450 Planarity : 0.002 0.009 270 Dihedral : 41.741 179.855 315 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.96 % Allowed : 31.11 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.69), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.27 (0.53), residues: 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.31 ( 2340) covalent geometry : angle 0.76789 / 0.37 ( 3015) hydrogen bonds : bond 0.09447 / 6.05 ( 37) hydrogen bonds : angle 9.12021 / 5.53 ( 111) Misc. bond : bond 0.00095 / 0.06 ( 45) =============================================================================== Job complete usr+sys time: 1616.78 seconds wall clock time: 28 minutes 14.02 seconds (1694.02 seconds total)