Starting phenix.real_space_refine on Sat May 10 07:21:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cz3_46060/05_2025/9cz3_46060_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cz3_46060/05_2025/9cz3_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_46060/05_2025/9cz3_46060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cz3_46060/05_2025/9cz3_46060.map" model { file = "/net/cci-nas-00/data/ceres_data/9cz3_46060/05_2025/9cz3_46060_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cz3_46060/05_2025/9cz3_46060_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.58, per 1000 atoms: 0.64 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: 1.44 Conformation dependent library (CDL) restraints added in 231.9 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: 0.59 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: 1.70 Time building geometry restraints manager: 1.73 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: 0.010 Normalize map: mean=0, sd=1: 6.220 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.870 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 hydrogen bonds : bond 0.32649 ( 37) hydrogen bonds : angle 12.79465 ( 111) covalent geometry : bond 0.01406 ( 2340) covalent geometry : angle 1.85807 ( 3015) Misc. bond : bond 0.10222 ( 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 : 0.421 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: 4.3615 time to fit residues: 344.6514 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 : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.070141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.067240 restraints weight = 55426.702| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.66 r_work: 0.3846 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.8619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.199 2385 Z= 2.284 Angle : 2.841 13.934 3015 Z= 1.328 Chirality : 0.153 0.414 450 Planarity : 0.009 0.035 270 Dihedral : 41.426 179.903 315 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 39.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 12.22 % Allowed : 20.74 % Favored : 67.04 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.60), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.42 (0.46), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.20484 ( 37) hydrogen bonds : angle 12.60526 ( 111) covalent geometry : bond 0.06037 ( 2340) covalent geometry : angle 2.84122 ( 3015) Misc. bond : bond 0.00780 ( 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 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 16 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.9445 (pttt) cc_final: 0.8920 (mttp) REVERT: C 1 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6062 (mmtm) REVERT: C 6 LYS cc_start: 0.8206 (tttt) cc_final: 0.7007 (pttt) REVERT: H 6 LYS cc_start: 0.9138 (mptt) cc_final: 0.8474 (pmtt) REVERT: I 6 LYS cc_start: 0.8098 (pttt) cc_final: 0.7447 (mptt) REVERT: c 6 LYS cc_start: 0.9395 (pttt) cc_final: 0.8885 (tptt) REVERT: d 1 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.6120 (mmtp) REVERT: d 6 LYS cc_start: 0.7867 (tttt) cc_final: 0.6410 (pttt) REVERT: i 6 LYS cc_start: 0.9392 (mptt) cc_final: 0.8618 (pmtt) REVERT: j 6 LYS cc_start: 0.8328 (tttt) cc_final: 0.6665 (mmpt) REVERT: l 6 LYS cc_start: 0.5376 (OUTLIER) cc_final: 0.4184 (mptt) REVERT: m 1 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5738 (mmtp) REVERT: m 6 LYS cc_start: 0.8004 (tttt) cc_final: 0.7399 (pttt) outliers start: 33 outliers final: 17 residues processed: 49 average time/residue: 3.2673 time to fit residues: 163.1764 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 14 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain d residue 1 LYS Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.070564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.067695 restraints weight = 56738.917| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.69 r_work: 0.3857 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.9566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.192 2385 Z= 2.294 Angle : 2.853 14.404 3015 Z= 1.349 Chirality : 0.154 0.428 450 Planarity : 0.009 0.026 270 Dihedral : 41.732 179.801 315 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 44.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 16.30 % Allowed : 26.67 % Favored : 57.04 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.45 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19671 ( 37) hydrogen bonds : angle 12.23374 ( 111) covalent geometry : bond 0.06066 ( 2340) covalent geometry : angle 2.85301 ( 3015) Misc. bond : bond 0.00772 ( 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 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 11 time to evaluate : 0.466 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: F 1 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8354 (ttmm) REVERT: F 6 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7118 (mtpt) REVERT: H 6 LYS cc_start: 0.9164 (mptt) cc_final: 0.8470 (pmtt) REVERT: I 6 LYS cc_start: 0.7971 (pttt) cc_final: 0.7395 (mptt) REVERT: R 3 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7306 (pp) REVERT: c 1 LYS cc_start: 0.5145 (OUTLIER) cc_final: 0.4937 (pptt) REVERT: i 6 LYS cc_start: 0.9387 (mptt) cc_final: 0.8542 (pmtt) REVERT: l 6 LYS cc_start: 0.5433 (OUTLIER) cc_final: 0.4625 (mptt) REVERT: m 1 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5705 (mmtp) outliers start: 44 outliers final: 24 residues processed: 54 average time/residue: 2.7923 time to fit residues: 153.9751 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 11 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain E residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain F residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain c residue 1 LYS Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain p residue 1 LYS Chi-restraints excluded: chain r residue 3 ILE 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: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.073766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.071027 restraints weight = 58730.820| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.36 r_work: 0.3915 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.9910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.198 2385 Z= 2.307 Angle : 2.857 14.947 3015 Z= 1.346 Chirality : 0.154 0.442 450 Planarity : 0.009 0.029 270 Dihedral : 41.869 179.939 315 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 45.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 17.04 % Allowed : 30.37 % Favored : 52.59 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19633 ( 37) hydrogen bonds : angle 12.10915 ( 111) covalent geometry : bond 0.06080 ( 2340) covalent geometry : angle 2.85705 ( 3015) Misc. bond : bond 0.00742 ( 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 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 11 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.9453 (pttt) cc_final: 0.8829 (tttt) REVERT: C 1 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.5943 (mmtp) REVERT: F 1 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8150 (ttmm) REVERT: F 6 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7157 (mtpt) REVERT: H 6 LYS cc_start: 0.9098 (mptt) cc_final: 0.8441 (pmtt) REVERT: I 6 LYS cc_start: 0.7991 (pttt) cc_final: 0.7351 (mptt) REVERT: R 3 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7326 (pp) REVERT: c 6 LYS cc_start: 0.9316 (pttt) cc_final: 0.8724 (tttt) REVERT: i 6 LYS cc_start: 0.9342 (mptt) cc_final: 0.8590 (pmtt) REVERT: j 3 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8087 (pp) REVERT: l 6 LYS cc_start: 0.4986 (OUTLIER) cc_final: 0.4578 (mptt) REVERT: m 1 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5865 (mmtp) REVERT: s 1 LYS cc_start: 0.6444 (OUTLIER) cc_final: 0.5796 (pmtt) outliers start: 46 outliers final: 26 residues processed: 56 average time/residue: 2.5745 time to fit residues: 147.7506 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 10 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain E residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain F residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain d residue 1 LYS Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain p residue 1 LYS Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 1 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.073787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.070907 restraints weight = 58068.738| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.65 r_work: 0.3966 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 1.0156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.194 2385 Z= 2.299 Angle : 2.829 13.864 3015 Z= 1.340 Chirality : 0.155 0.445 450 Planarity : 0.009 0.027 270 Dihedral : 41.861 179.648 315 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 47.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 20.00 % Allowed : 31.85 % Favored : 48.15 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19557 ( 37) hydrogen bonds : angle 12.12805 ( 111) covalent geometry : bond 0.06058 ( 2340) covalent geometry : angle 2.82874 ( 3015) Misc. bond : bond 0.00764 ( 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 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 10 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6564 (pptt) REVERT: B 6 LYS cc_start: 0.9404 (pttt) cc_final: 0.8801 (tttt) REVERT: F 1 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8274 (ttmm) REVERT: F 6 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7073 (mtpt) REVERT: H 6 LYS cc_start: 0.9096 (mptt) cc_final: 0.8419 (pmtt) REVERT: I 1 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.3323 (pptt) REVERT: I 6 LYS cc_start: 0.7952 (pttt) cc_final: 0.7330 (mptt) REVERT: L 2 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9190 (mm) REVERT: R 3 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7201 (pp) REVERT: c 6 LYS cc_start: 0.9339 (pttt) cc_final: 0.8705 (tttt) REVERT: d 1 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.6032 (mmtp) REVERT: i 6 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8560 (pmtt) REVERT: l 6 LYS cc_start: 0.4837 (OUTLIER) cc_final: 0.4491 (mptt) REVERT: m 1 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5770 (mmtp) REVERT: s 1 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5723 (pmtt) outliers start: 54 outliers final: 32 residues processed: 62 average time/residue: 2.2454 time to fit residues: 142.9632 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 10 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS 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 C residue 3 ILE Chi-restraints excluded: chain E residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain F residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain T residue 1 LYS Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain d residue 1 LYS Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain p residue 1 LYS Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r 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: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.072963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.070061 restraints weight = 57726.811| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.62 r_work: 0.3876 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 1.0279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.197 2385 Z= 2.297 Angle : 2.820 14.410 3015 Z= 1.336 Chirality : 0.155 0.447 450 Planarity : 0.009 0.030 270 Dihedral : 41.858 179.696 315 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 48.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 20.37 % Allowed : 31.48 % Favored : 48.15 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19566 ( 37) hydrogen bonds : angle 12.06533 ( 111) covalent geometry : bond 0.06051 ( 2340) covalent geometry : angle 2.82027 ( 3015) Misc. bond : bond 0.00756 ( 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 65 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 10 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.9430 (pttt) cc_final: 0.8833 (tttt) REVERT: F 1 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8186 (ttmm) REVERT: F 6 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7185 (mtpt) REVERT: H 6 LYS cc_start: 0.9168 (mptt) cc_final: 0.8437 (pmtt) REVERT: I 6 LYS cc_start: 0.8063 (pttt) cc_final: 0.7386 (mptt) REVERT: L 2 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9199 (mm) REVERT: L 6 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7448 (pttt) REVERT: R 3 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7263 (pp) REVERT: c 6 LYS cc_start: 0.9394 (pttt) cc_final: 0.8716 (tttt) REVERT: i 6 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.8598 (pmtt) REVERT: m 1 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.5821 (mmtp) REVERT: s 1 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5712 (pmtt) outliers start: 55 outliers final: 33 residues processed: 63 average time/residue: 2.1587 time to fit residues: 139.7980 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 10 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS 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 E residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain F residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain T residue 1 LYS Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain d residue 1 LYS Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain p residue 1 LYS Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r 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: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.072654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.070078 restraints weight = 57410.411| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.46 r_work: 0.3927 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 1.0375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.198 2385 Z= 2.294 Angle : 2.831 15.360 3015 Z= 1.342 Chirality : 0.155 0.447 450 Planarity : 0.010 0.030 270 Dihedral : 41.908 179.433 315 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 50.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 19.63 % Allowed : 32.96 % Favored : 47.41 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.62), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19564 ( 37) hydrogen bonds : angle 12.11289 ( 111) covalent geometry : bond 0.06041 ( 2340) covalent geometry : angle 2.83085 ( 3015) Misc. bond : bond 0.00753 ( 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 63 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 10 time to evaluate : 0.508 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: 0.9434 (pttt) cc_final: 0.8828 (tttt) REVERT: F 1 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8144 (ttmm) REVERT: F 6 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7179 (mtpt) REVERT: H 6 LYS cc_start: 0.9128 (mptt) cc_final: 0.8440 (pmtt) REVERT: I 1 LYS cc_start: 0.4971 (OUTLIER) cc_final: 0.3194 (pttt) REVERT: I 6 LYS cc_start: 0.8023 (pttt) cc_final: 0.7361 (mptt) REVERT: L 2 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9180 (mm) REVERT: L 6 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7477 (pttt) REVERT: R 3 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7269 (pp) REVERT: c 6 LYS cc_start: 0.9398 (pttt) cc_final: 0.8711 (mttp) REVERT: d 6 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.6221 (pttt) REVERT: i 6 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8598 (pmtt) REVERT: m 1 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.5810 (mmtp) REVERT: s 1 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5675 (pmtt) outliers start: 53 outliers final: 37 residues processed: 61 average time/residue: 2.3538 time to fit residues: 147.5075 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 10 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS 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 E residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain F residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain T residue 1 LYS Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain d residue 1 LYS Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 1 LYS Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain p residue 1 LYS Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r 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: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.072713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.069965 restraints weight = 56964.069| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.78 r_work: 0.3910 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 1.0426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.198 2385 Z= 2.299 Angle : 2.834 15.457 3015 Z= 1.343 Chirality : 0.155 0.446 450 Planarity : 0.009 0.029 270 Dihedral : 41.931 179.454 315 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 50.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 22.22 % Allowed : 30.37 % Favored : 47.41 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19483 ( 37) hydrogen bonds : angle 12.08376 ( 111) covalent geometry : bond 0.06053 ( 2340) covalent geometry : angle 2.83399 ( 3015) Misc. bond : bond 0.00754 ( 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 70 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 10 time to evaluate : 0.522 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: symmetry clash REVERT: B 6 LYS cc_start: 0.9464 (pttt) cc_final: 0.8852 (tttt) REVERT: F 1 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8135 (ttmm) REVERT: F 6 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7276 (mtpt) REVERT: H 6 LYS cc_start: 0.9156 (mptt) cc_final: 0.8442 (pmtt) REVERT: I 1 LYS cc_start: 0.4968 (OUTLIER) cc_final: 0.3446 (pptt) REVERT: I 6 LYS cc_start: 0.8079 (pttt) cc_final: 0.7377 (mptt) REVERT: L 2 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9180 (mm) REVERT: L 6 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7474 (pttt) REVERT: R 3 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7304 (pp) REVERT: c 6 LYS cc_start: 0.9444 (pttt) cc_final: 0.8724 (mttp) REVERT: i 6 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.8607 (pmtt) REVERT: m 1 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5872 (mmtp) REVERT: s 1 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5708 (pmtt) outliers start: 60 outliers final: 38 residues processed: 68 average time/residue: 2.2085 time to fit residues: 154.3519 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 10 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS 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 C residue 4 ILE Chi-restraints excluded: chain E residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain F residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain T residue 1 LYS Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain d residue 1 LYS Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 1 LYS Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain p residue 1 LYS Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r 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: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.072841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.070366 restraints weight = 57680.944| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.17 r_work: 0.3940 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 1.0465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.198 2385 Z= 2.295 Angle : 2.838 15.485 3015 Z= 1.343 Chirality : 0.155 0.439 450 Planarity : 0.010 0.030 270 Dihedral : 41.926 179.503 315 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 50.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 20.37 % Allowed : 32.96 % Favored : 46.67 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19444 ( 37) hydrogen bonds : angle 12.08352 ( 111) covalent geometry : bond 0.06040 ( 2340) covalent geometry : angle 2.83752 ( 3015) Misc. bond : bond 0.00739 ( 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 65 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 10 time to evaluate : 0.493 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: 0.9420 (pttt) cc_final: 0.8852 (tttt) REVERT: F 1 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8136 (ttmm) REVERT: F 6 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7183 (mtpt) REVERT: H 6 LYS cc_start: 0.9109 (mptt) cc_final: 0.8424 (pmtt) REVERT: I 1 LYS cc_start: 0.5002 (OUTLIER) cc_final: 0.3309 (pttt) REVERT: I 6 LYS cc_start: 0.8020 (pttt) cc_final: 0.7349 (mptt) REVERT: L 2 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9172 (mm) REVERT: L 6 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7433 (pttt) REVERT: R 3 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7266 (pp) REVERT: c 6 LYS cc_start: 0.9399 (pttt) cc_final: 0.8712 (mttp) REVERT: d 6 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.6352 (pttt) REVERT: i 6 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8597 (pmtt) REVERT: m 1 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5831 (mmtp) REVERT: s 1 LYS cc_start: 0.6289 (OUTLIER) cc_final: 0.5688 (pmtt) outliers start: 55 outliers final: 38 residues processed: 63 average time/residue: 2.1335 time to fit residues: 138.1389 Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 10 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS 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 C residue 4 ILE Chi-restraints excluded: chain E residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain F residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain T residue 1 LYS Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain d residue 1 LYS Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 1 LYS Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain p residue 1 LYS Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r 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: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.072652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.070187 restraints weight = 57572.952| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 3.16 r_work: 0.3939 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 1.0495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.199 2385 Z= 2.296 Angle : 2.833 15.503 3015 Z= 1.342 Chirality : 0.156 0.432 450 Planarity : 0.009 0.030 270 Dihedral : 42.008 179.281 315 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 51.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 19.63 % Allowed : 33.70 % Favored : 46.67 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19494 ( 37) hydrogen bonds : angle 12.07958 ( 111) covalent geometry : bond 0.06039 ( 2340) covalent geometry : angle 2.83305 ( 3015) Misc. bond : bond 0.00751 ( 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 63 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 10 time to evaluate : 0.522 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: 0.9424 (pttt) cc_final: 0.8851 (tttt) REVERT: F 1 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: F 6 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7225 (mtpt) REVERT: H 6 LYS cc_start: 0.9110 (mptt) cc_final: 0.8423 (pmtt) REVERT: I 1 LYS cc_start: 0.5047 (OUTLIER) cc_final: 0.3041 (pttt) REVERT: I 6 LYS cc_start: 0.8015 (pttt) cc_final: 0.7342 (mptt) REVERT: L 2 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9164 (mm) REVERT: L 6 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7428 (pttt) REVERT: R 1 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.4839 (pptt) REVERT: R 3 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7254 (pp) REVERT: c 6 LYS cc_start: 0.9405 (pttt) cc_final: 0.8729 (tttt) REVERT: d 6 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.6350 (pttt) REVERT: i 6 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.8596 (pmtt) REVERT: m 1 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5819 (mmtp) REVERT: r 6 LYS cc_start: 0.4985 (OUTLIER) cc_final: 0.4526 (pmtt) REVERT: s 1 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5694 (pmtt) outliers start: 53 outliers final: 38 residues processed: 61 average time/residue: 2.2543 time to fit residues: 141.1296 Evaluate side-chains 60 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 10 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS 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 C residue 4 ILE Chi-restraints excluded: chain E residue 1 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain F residue 1 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 1 LYS Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain T residue 1 LYS Chi-restraints excluded: chain U residue 1 LYS Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain V residue 2 ILE Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain d residue 1 LYS Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 1 LYS Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain p residue 1 LYS Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain r residue 6 LYS 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: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.072666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.070195 restraints weight = 58049.194| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.16 r_work: 0.3937 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 1.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.198 2385 Z= 2.292 Angle : 2.830 15.499 3015 Z= 1.341 Chirality : 0.155 0.434 450 Planarity : 0.009 0.030 270 Dihedral : 41.999 179.349 315 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 51.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 20.00 % Allowed : 33.70 % Favored : 46.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.48), residues: 180 Details of bonding type rmsd hydrogen bonds : bond 0.19467 ( 37) hydrogen bonds : angle 12.08377 ( 111) covalent geometry : bond 0.06032 ( 2340) covalent geometry : angle 2.82977 ( 3015) Misc. bond : bond 0.00753 ( 45) =============================================================================== Job complete usr+sys time: 3546.55 seconds wall clock time: 61 minutes 29.63 seconds (3689.63 seconds total)