Starting phenix.real_space_refine on Tue Feb 3 12:26:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d2n_46501/02_2026/9d2n_46501.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d2n_46501/02_2026/9d2n_46501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d2n_46501/02_2026/9d2n_46501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d2n_46501/02_2026/9d2n_46501.map" model { file = "/net/cci-nas-00/data/ceres_data/9d2n_46501/02_2026/9d2n_46501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d2n_46501/02_2026/9d2n_46501.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1476 2.51 5 N 324 2.21 5 O 252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2052 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 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} Time building chain proxies: 0.63, per 1000 atoms: 0.31 Number of scatterers: 2052 At special positions: 0 Unit cell: (86.9, 86.9, 31.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 252 8.00 N 324 7.00 C 1476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=36, symmetry=0 Number of additional bonds: simple=36, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 58.8 milliseconds 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 432 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.324A pdb=" N ILE A 3 " --> pdb=" O ILE M 4 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE M 3 " --> pdb=" O ILE Y 4 " (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 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.304A pdb=" N ILE C 3 " --> pdb=" O ILE O 4 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE O 3 " --> pdb=" O ILE a 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.395A pdb=" N ILE D 3 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE P 3 " --> pdb=" O ILE b 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.275A pdb=" N ILE F 3 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE R 3 " --> pdb=" O ILE d 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 3 through 5 removed outlier: 6.242A pdb=" N ILE G 3 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE S 3 " --> pdb=" O ILE e 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 5 Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 5 removed outlier: 6.271A pdb=" N ILE I 3 " --> pdb=" O ILE U 4 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE U 3 " --> pdb=" O ILE g 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 3 through 5 removed outlier: 6.387A pdb=" N ILE J 3 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE V 3 " --> pdb=" O ILE h 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'L' and resid 2 through 5 removed outlier: 6.330A pdb=" N ILE L 3 " --> pdb=" O ILE X 4 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE X 3 " --> pdb=" O ILE j 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.19 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 252 1.27 - 1.34: 190 1.34 - 1.41: 242 1.41 - 1.48: 215 1.48 - 1.55: 1117 Bond restraints: 2016 Sorted by residual: bond pdb=" N LYS g 1 " pdb=" CA LYS g 1 " ideal model delta sigma weight residual 1.458 1.540 -0.082 1.90e-02 2.77e+03 1.86e+01 bond pdb=" N LYS d 1 " pdb=" CA LYS d 1 " ideal model delta sigma weight residual 1.458 1.538 -0.080 1.90e-02 2.77e+03 1.77e+01 bond pdb=" N LYS U 1 " pdb=" CA LYS U 1 " ideal model delta sigma weight residual 1.458 1.536 -0.078 1.90e-02 2.77e+03 1.70e+01 bond pdb=" N LYS F 1 " pdb=" CA LYS F 1 " ideal model delta sigma weight residual 1.458 1.536 -0.078 1.90e-02 2.77e+03 1.68e+01 bond pdb=" N LYS L 1 " pdb=" CA LYS L 1 " ideal model delta sigma weight residual 1.458 1.536 -0.078 1.90e-02 2.77e+03 1.67e+01 ... (remaining 2011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 1865 1.86 - 3.72: 611 3.72 - 5.58: 95 5.58 - 7.44: 9 7.44 - 9.31: 12 Bond angle restraints: 2592 Sorted by residual: angle pdb=" CA PHE N 5 " pdb=" CB PHE N 5 " pdb=" CG PHE N 5 " ideal model delta sigma weight residual 113.80 119.93 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" CA PHE Z 5 " pdb=" CB PHE Z 5 " pdb=" CG PHE Z 5 " ideal model delta sigma weight residual 113.80 119.41 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA PHE Q 5 " pdb=" CB PHE Q 5 " pdb=" CG PHE Q 5 " ideal model delta sigma weight residual 113.80 118.51 -4.71 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N PHE C 5 " pdb=" CA PHE C 5 " pdb=" C PHE C 5 " ideal model delta sigma weight residual 108.60 115.40 -6.80 1.46e+00 4.69e-01 2.17e+01 angle pdb=" CA PHE C 5 " pdb=" CB PHE C 5 " pdb=" CG PHE C 5 " ideal model delta sigma weight residual 113.80 118.45 -4.65 1.00e+00 1.00e+00 2.16e+01 ... (remaining 2587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 1234 35.80 - 71.60: 14 71.60 - 107.40: 0 107.40 - 143.20: 0 143.20 - 179.00: 12 Dihedral angle restraints: 1260 sinusoidal: 648 harmonic: 612 Sorted by residual: dihedral pdb=" CH3 ACE Q 0 " pdb=" C ACE Q 0 " pdb=" N LYS Q 1 " pdb=" CA LYS Q 1 " ideal model delta sinusoidal sigma weight residual -180.00 -1.00 -179.00 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE K 0 " pdb=" C ACE K 0 " pdb=" N LYS K 1 " pdb=" CA LYS K 1 " ideal model delta sinusoidal sigma weight residual -180.00 -1.50 -178.50 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 2.57 177.43 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 132 0.066 - 0.133: 104 0.133 - 0.199: 42 0.199 - 0.266: 40 0.266 - 0.332: 6 Chirality restraints: 324 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 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA LYS a 1 " pdb=" N LYS a 1 " pdb=" C LYS a 1 " pdb=" CB LYS a 1 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LYS d 1 " pdb=" N LYS d 1 " pdb=" C LYS d 1 " pdb=" CB LYS d 1 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 321 not shown) Planarity restraints: 252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE N 0 " 0.052 2.00e-02 2.50e+03 4.47e-02 2.50e+01 pdb=" O ACE N 0 " 0.008 2.00e-02 2.50e+03 pdb=" CH3 ACE N 0 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS N 1 " -0.072 2.00e-02 2.50e+03 pdb=" CA LYS N 1 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 5 " 0.060 2.00e-02 2.50e+03 3.69e-02 2.39e+01 pdb=" CG PHE B 5 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B 5 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE B 5 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE B 5 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 5 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 5 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE a 0 " -0.010 2.00e-02 2.50e+03 3.79e-02 1.80e+01 pdb=" O ACE a 0 " 0.017 2.00e-02 2.50e+03 pdb=" CH3 ACE a 0 " -0.029 2.00e-02 2.50e+03 pdb=" N LYS a 1 " 0.064 2.00e-02 2.50e+03 pdb=" CA LYS a 1 " -0.043 2.00e-02 2.50e+03 ... (remaining 249 not shown) Histogram of nonbonded interaction distances: 2.69 - 3.13: 1189 3.13 - 3.58: 1780 3.58 - 4.02: 2469 4.02 - 4.46: 2490 4.46 - 4.90: 5017 Nonbonded interactions: 12945 Sorted by model distance: nonbonded pdb=" O ILE U 4 " pdb=" CA PHE U 5 " model vdw 2.692 2.776 nonbonded pdb=" O ILE X 4 " pdb=" CA PHE X 5 " model vdw 2.696 2.776 nonbonded pdb=" O ILE O 4 " pdb=" CA PHE O 5 " model vdw 2.698 2.776 nonbonded pdb=" O ILE R 4 " pdb=" CA PHE R 5 " model vdw 2.699 2.776 nonbonded pdb=" O ILE a 4 " pdb=" CA PHE a 5 " model vdw 2.701 2.776 ... (remaining 12940 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.400 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.019 0.108 2052 Z= 1.463 Angle : 1.835 9.305 2592 Z= 1.157 Chirality : 0.121 0.332 324 Planarity : 0.013 0.045 252 Dihedral : 23.602 179.000 828 Min Nonbonded Distance : 2.692 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.53), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.68 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.060 0.012 PHE B 5 Details of bonding type rmsd covalent geometry : bond 0.01353 ( 2016) covalent geometry : angle 1.83536 ( 2592) hydrogen bonds : bond 0.14471 ( 24) hydrogen bonds : angle 5.21544 ( 72) Misc. bond : bond 0.09761 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.068 Fit side-chains REVERT: R 2 ILE cc_start: 0.8979 (tt) cc_final: 0.8566 (pt) REVERT: U 2 ILE cc_start: 0.8994 (tt) cc_final: 0.8526 (pt) REVERT: X 2 ILE cc_start: 0.8847 (tt) cc_final: 0.8534 (pt) REVERT: a 1 LYS cc_start: 0.8825 (tttt) cc_final: 0.8346 (tttp) REVERT: d 5 PHE cc_start: 0.8392 (p90) cc_final: 0.8089 (p90) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0662 time to fit residues: 2.3727 Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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: 0.9980 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 = 0.3209 r_free = 0.3209 target = 0.076823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.061447 restraints weight = 4752.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.063607 restraints weight = 2902.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.065120 restraints weight = 2172.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066163 restraints weight = 1782.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.066931 restraints weight = 1541.767| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.443 2052 Z= 4.849 Angle : 4.907 25.671 2592 Z= 2.481 Chirality : 0.331 0.798 324 Planarity : 0.022 0.060 252 Dihedral : 27.471 179.537 252 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 74.45 Ramachandran Plot: Outliers : 2.08 % Allowed : 25.00 % Favored : 72.92 % Rotamer: Outliers : 20.83 % Allowed : 13.89 % Favored : 65.28 % Cbeta Deviations : 2.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.26 (0.52), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.76 (0.40), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.135 0.029 PHE W 5 Details of bonding type rmsd covalent geometry : bond 0.12454 ( 2016) covalent geometry : angle 4.90717 ( 2592) hydrogen bonds : bond 0.14744 ( 24) hydrogen bonds : angle 6.29368 ( 72) Misc. bond : bond 0.01212 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 41 time to evaluate : 0.056 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: G 1 LYS cc_start: 0.8123 (mttt) cc_final: 0.7398 (mmtm) REVERT: X 5 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8537 (p90) REVERT: b 5 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7972 (p90) REVERT: d 5 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8504 (p90) outliers start: 45 outliers final: 40 residues processed: 82 average time/residue: 0.0934 time to fit residues: 8.3330 Evaluate side-chains 79 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 36 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.3218 r_free = 0.3218 target = 0.076978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.061283 restraints weight = 4752.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.063606 restraints weight = 2950.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.065173 restraints weight = 2206.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066275 restraints weight = 1809.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.067040 restraints weight = 1564.089| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.443 2052 Z= 4.825 Angle : 4.884 22.710 2592 Z= 2.471 Chirality : 0.318 0.799 324 Planarity : 0.022 0.100 252 Dihedral : 26.679 179.528 252 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 71.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.28 % Favored : 59.72 % Rotamer: Outliers : 30.56 % Allowed : 19.91 % Favored : 49.54 % Cbeta Deviations : 4.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.50 (0.47), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.71 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.117 0.028 PHE W 5 Details of bonding type rmsd covalent geometry : bond 0.12455 ( 2016) covalent geometry : angle 4.88407 ( 2592) hydrogen bonds : bond 0.16040 ( 24) hydrogen bonds : angle 6.42583 ( 72) Misc. bond : bond 0.01280 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 43 time to evaluate : 0.056 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: K 1 LYS cc_start: 0.9089 (tttt) cc_final: 0.8874 (mtpt) REVERT: T 6 LYS cc_start: 0.9355 (tttt) cc_final: 0.9000 (tttp) REVERT: Z 5 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7857 (m-10) REVERT: a 5 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8539 (p90) REVERT: b 1 LYS cc_start: 0.8522 (mttt) cc_final: 0.7766 (mmtp) REVERT: b 5 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8110 (p90) REVERT: d 5 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8534 (p90) REVERT: e 1 LYS cc_start: 0.8584 (mttt) cc_final: 0.7623 (mmtm) outliers start: 66 outliers final: 60 residues processed: 105 average time/residue: 0.0856 time to fit residues: 9.8461 Evaluate side-chains 107 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 43 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 5 PHE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.076760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.061290 restraints weight = 4668.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.063578 restraints weight = 2931.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.065085 restraints weight = 2214.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.066161 restraints weight = 1827.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.066973 restraints weight = 1585.684| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.442 2052 Z= 4.813 Angle : 4.874 24.885 2592 Z= 2.462 Chirality : 0.318 0.794 324 Planarity : 0.021 0.059 252 Dihedral : 25.223 178.434 252 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 72.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 42.36 % Favored : 57.64 % Rotamer: Outliers : 31.94 % Allowed : 21.76 % Favored : 46.30 % Cbeta Deviations : 3.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.63 (0.46), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.81 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.114 0.027 PHE I 5 Details of bonding type rmsd covalent geometry : bond 0.12427 ( 2016) covalent geometry : angle 4.87420 ( 2592) hydrogen bonds : bond 0.15840 ( 24) hydrogen bonds : angle 6.52283 ( 72) Misc. bond : bond 0.01302 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 44 time to evaluate : 0.092 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 LYS cc_start: 0.8456 (mttt) cc_final: 0.8243 (mmtt) REVERT: G 1 LYS cc_start: 0.8423 (mttt) cc_final: 0.7647 (mmtp) REVERT: T 6 LYS cc_start: 0.9355 (tttt) cc_final: 0.9109 (ttpt) REVERT: Z 5 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: b 5 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8160 (p90) REVERT: d 5 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8420 (p90) outliers start: 69 outliers final: 66 residues processed: 108 average time/residue: 0.0833 time to fit residues: 9.9259 Evaluate side-chains 113 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 44 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 5 PHE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.3209 r_free = 0.3209 target = 0.076375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.061111 restraints weight = 4701.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.063316 restraints weight = 2981.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.064827 restraints weight = 2251.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.065891 restraints weight = 1854.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066678 restraints weight = 1606.573| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.7196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.443 2052 Z= 4.814 Angle : 4.897 25.253 2592 Z= 2.467 Chirality : 0.318 0.804 324 Planarity : 0.020 0.061 252 Dihedral : 25.189 178.885 252 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 74.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 42.36 % Favored : 57.64 % Rotamer: Outliers : 34.26 % Allowed : 23.15 % Favored : 42.59 % Cbeta Deviations : 5.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.76 (0.46), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.91 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.027 PHE I 5 Details of bonding type rmsd covalent geometry : bond 0.12413 ( 2016) covalent geometry : angle 4.89695 ( 2592) hydrogen bonds : bond 0.16015 ( 24) hydrogen bonds : angle 6.45546 ( 72) Misc. bond : bond 0.01290 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 44 time to evaluate : 0.094 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 1 LYS cc_start: 0.8461 (mttt) cc_final: 0.7658 (mmtp) REVERT: T 6 LYS cc_start: 0.9347 (tttt) cc_final: 0.9095 (ttpt) REVERT: Z 5 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7853 (m-10) REVERT: b 5 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8138 (p90) REVERT: d 5 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8356 (p90) outliers start: 74 outliers final: 68 residues processed: 112 average time/residue: 0.0884 time to fit residues: 10.9188 Evaluate side-chains 115 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 44 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 5 PHE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 4 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.076080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.061140 restraints weight = 4592.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.063254 restraints weight = 2993.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.064675 restraints weight = 2285.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.065709 restraints weight = 1892.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.066484 restraints weight = 1647.616| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.439 2052 Z= 4.810 Angle : 4.862 24.669 2592 Z= 2.450 Chirality : 0.317 0.792 324 Planarity : 0.020 0.060 252 Dihedral : 25.211 179.779 252 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 74.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 42.36 % Favored : 57.64 % Rotamer: Outliers : 34.72 % Allowed : 24.07 % Favored : 41.20 % Cbeta Deviations : 4.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.82 (0.45), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.027 PHE I 5 Details of bonding type rmsd covalent geometry : bond 0.12409 ( 2016) covalent geometry : angle 4.86233 ( 2592) hydrogen bonds : bond 0.15923 ( 24) hydrogen bonds : angle 6.46230 ( 72) Misc. bond : bond 0.01276 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 44 time to evaluate : 0.096 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: symmetry clash revert: symmetry clash REVERT: D 1 LYS cc_start: 0.8613 (mmtt) cc_final: 0.7909 (mmtp) REVERT: G 1 LYS cc_start: 0.8474 (mttt) cc_final: 0.7675 (mmtp) REVERT: T 6 LYS cc_start: 0.9344 (tttt) cc_final: 0.9097 (tttp) REVERT: Z 5 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.7888 (m-10) REVERT: b 1 LYS cc_start: 0.8508 (mttt) cc_final: 0.7871 (mmtp) REVERT: b 5 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8144 (p90) REVERT: d 5 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8364 (p90) outliers start: 75 outliers final: 70 residues processed: 111 average time/residue: 0.0897 time to fit residues: 11.0014 Evaluate side-chains 117 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 44 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 1 LYS Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 5 PHE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.076658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.061225 restraints weight = 4614.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.063468 restraints weight = 2903.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065073 restraints weight = 2185.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.066161 restraints weight = 1782.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.066982 restraints weight = 1537.655| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.437 2052 Z= 4.813 Angle : 4.867 24.789 2592 Z= 2.454 Chirality : 0.318 0.799 324 Planarity : 0.020 0.061 252 Dihedral : 25.206 179.683 252 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 75.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.06 % Favored : 56.94 % Rotamer: Outliers : 34.72 % Allowed : 25.00 % Favored : 40.28 % Cbeta Deviations : 5.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.81 (0.45), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.95 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.027 PHE I 5 Details of bonding type rmsd covalent geometry : bond 0.12413 ( 2016) covalent geometry : angle 4.86706 ( 2592) hydrogen bonds : bond 0.16021 ( 24) hydrogen bonds : angle 6.47622 ( 72) Misc. bond : bond 0.01269 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 44 time to evaluate : 0.057 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: symmetry clash revert: symmetry clash REVERT: D 1 LYS cc_start: 0.8609 (mmtt) cc_final: 0.7831 (mmtp) REVERT: G 1 LYS cc_start: 0.8462 (mttt) cc_final: 0.7626 (mmtp) REVERT: T 6 LYS cc_start: 0.9360 (tttt) cc_final: 0.9136 (tppp) REVERT: Z 5 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.7859 (m-10) REVERT: b 1 LYS cc_start: 0.8553 (mttt) cc_final: 0.7915 (mmtp) REVERT: b 5 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8180 (p90) REVERT: d 5 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8345 (p90) outliers start: 75 outliers final: 72 residues processed: 112 average time/residue: 0.0603 time to fit residues: 7.4567 Evaluate side-chains 119 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 44 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain R residue 1 LYS Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 5 PHE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 4 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 4 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.076589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.061115 restraints weight = 4640.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.063380 restraints weight = 2919.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.064929 restraints weight = 2196.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.065998 restraints weight = 1806.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066817 restraints weight = 1565.092| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.437 2052 Z= 4.812 Angle : 4.860 24.633 2592 Z= 2.449 Chirality : 0.317 0.789 324 Planarity : 0.020 0.061 252 Dihedral : 25.229 179.876 252 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 76.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.06 % Favored : 56.94 % Rotamer: Outliers : 35.19 % Allowed : 25.00 % Favored : 39.81 % Cbeta Deviations : 4.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.83 (0.45), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.027 PHE I 5 Details of bonding type rmsd covalent geometry : bond 0.12411 ( 2016) covalent geometry : angle 4.85963 ( 2592) hydrogen bonds : bond 0.16012 ( 24) hydrogen bonds : angle 6.48207 ( 72) Misc. bond : bond 0.01302 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 44 time to evaluate : 0.055 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: symmetry clash revert: symmetry clash REVERT: D 1 LYS cc_start: 0.8632 (mmtt) cc_final: 0.7826 (mmtp) REVERT: G 1 LYS cc_start: 0.8469 (mttt) cc_final: 0.7631 (mmtp) REVERT: T 6 LYS cc_start: 0.9362 (tttt) cc_final: 0.9048 (tppp) REVERT: Z 5 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: b 1 LYS cc_start: 0.8561 (mttt) cc_final: 0.7918 (mmtp) REVERT: b 5 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8181 (p90) REVERT: d 5 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8343 (p90) outliers start: 76 outliers final: 71 residues processed: 112 average time/residue: 0.0538 time to fit residues: 6.6775 Evaluate side-chains 118 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 44 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 5 PHE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 4 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.3214 r_free = 0.3214 target = 0.076628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.061180 restraints weight = 4624.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.063463 restraints weight = 2912.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.064982 restraints weight = 2194.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.066043 restraints weight = 1805.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066894 restraints weight = 1563.629| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.440 2052 Z= 4.813 Angle : 4.856 24.493 2592 Z= 2.449 Chirality : 0.317 0.792 324 Planarity : 0.020 0.061 252 Dihedral : 25.221 179.593 252 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 75.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.06 % Favored : 56.94 % Rotamer: Outliers : 35.19 % Allowed : 25.46 % Favored : 39.35 % Cbeta Deviations : 4.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.83 (0.45), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.027 PHE I 5 Details of bonding type rmsd covalent geometry : bond 0.12414 ( 2016) covalent geometry : angle 4.85609 ( 2592) hydrogen bonds : bond 0.16012 ( 24) hydrogen bonds : angle 6.48089 ( 72) Misc. bond : bond 0.01295 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 44 time to evaluate : 0.091 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: symmetry clash revert: symmetry clash REVERT: D 1 LYS cc_start: 0.8628 (mmtt) cc_final: 0.7847 (mmtp) REVERT: G 1 LYS cc_start: 0.8466 (mttt) cc_final: 0.7828 (mmtp) REVERT: T 6 LYS cc_start: 0.9363 (tttt) cc_final: 0.9116 (tttp) REVERT: Z 5 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.7859 (m-10) REVERT: b 1 LYS cc_start: 0.8561 (mttt) cc_final: 0.7916 (mmtp) REVERT: b 5 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8181 (p90) REVERT: d 5 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8343 (p90) outliers start: 76 outliers final: 72 residues processed: 112 average time/residue: 0.0597 time to fit residues: 7.4105 Evaluate side-chains 119 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 44 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 5 PHE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 4 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 4 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.076598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061211 restraints weight = 4674.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.063430 restraints weight = 2913.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.064980 restraints weight = 2190.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.065998 restraints weight = 1797.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066882 restraints weight = 1562.507| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.7276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.439 2052 Z= 4.813 Angle : 4.855 24.501 2592 Z= 2.448 Chirality : 0.317 0.790 324 Planarity : 0.020 0.061 252 Dihedral : 25.217 179.468 252 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 75.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.06 % Favored : 56.94 % Rotamer: Outliers : 35.19 % Allowed : 25.93 % Favored : 38.89 % Cbeta Deviations : 4.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.83 (0.45), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.027 PHE I 5 Details of bonding type rmsd covalent geometry : bond 0.12412 ( 2016) covalent geometry : angle 4.85547 ( 2592) hydrogen bonds : bond 0.16004 ( 24) hydrogen bonds : angle 6.48207 ( 72) Misc. bond : bond 0.01284 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 288 Ramachandran restraints generated. 144 Oldfield, 0 Emsley, 144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 44 time to evaluate : 0.055 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: symmetry clash revert: symmetry clash REVERT: D 1 LYS cc_start: 0.8630 (mmtt) cc_final: 0.7851 (mmtp) REVERT: G 1 LYS cc_start: 0.8465 (mttt) cc_final: 0.7628 (mmtp) REVERT: T 6 LYS cc_start: 0.9362 (tttt) cc_final: 0.9117 (tttp) REVERT: Z 5 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7859 (m-10) REVERT: b 1 LYS cc_start: 0.8561 (mttt) cc_final: 0.7919 (mmtp) REVERT: b 5 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8181 (p90) REVERT: d 5 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8346 (p90) outliers start: 76 outliers final: 72 residues processed: 113 average time/residue: 0.0561 time to fit residues: 7.0605 Evaluate side-chains 119 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 44 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 5 PHE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain V residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 5 PHE Chi-restraints excluded: chain a residue 2 ILE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 4 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 4 ILE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain e residue 3 ILE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 5 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.3213 r_free = 0.3213 target = 0.076599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.061214 restraints weight = 4644.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.063465 restraints weight = 2904.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.064987 restraints weight = 2182.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.066003 restraints weight = 1794.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.066861 restraints weight = 1560.223| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.123 0.438 2052 Z= 4.812 Angle : 4.855 24.486 2592 Z= 2.448 Chirality : 0.317 0.790 324 Planarity : 0.020 0.061 252 Dihedral : 25.208 179.307 252 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 75.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.06 % Favored : 56.94 % Rotamer: Outliers : 35.19 % Allowed : 25.93 % Favored : 38.89 % Cbeta Deviations : 4.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.83 (0.45), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.027 PHE I 5 Details of bonding type rmsd covalent geometry : bond 0.12412 ( 2016) covalent geometry : angle 4.85511 ( 2592) hydrogen bonds : bond 0.16011 ( 24) hydrogen bonds : angle 6.48299 ( 72) Misc. bond : bond 0.01289 ( 36) =============================================================================== Job complete usr+sys time: 347.27 seconds wall clock time: 6 minutes 42.39 seconds (402.39 seconds total)