Starting phenix.real_space_refine on Thu Oct 22 17:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d2n_46501/10_2026/9d2n_46501.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d2n_46501/10_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_46501/10_2026/9d2n_46501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d2n_46501/10_2026/9d2n_46501.map" model { file = "/net/cci-nas-00/data/ceres_data/9d2n_46501/10_2026/9d2n_46501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d2n_46501/10_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-2.3rc1-6221/lib/python3.11/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: 0.56, per 1000 atoms: 0.27 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: 0.14 Conformation dependent library (CDL) restraints added in 31.7 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: 0.05 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: 0.16 Time building geometry restraints manager: 0.15 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: 1.210 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: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.050 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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/Z covalent geometry : bond 0.01353 / 0.69 ( 2016) covalent geometry : angle 1.83536 / 1.16 ( 2592) hydrogen bonds : bond 0.14471 / 9.43 ( 24) hydrogen bonds : angle 5.21544 / 3.36 ( 72) Misc. bond : bond 0.09761 / 6.16 ( 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 : 0.059 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: 0.0648 time to fit residues: 2.3546 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 : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.115396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.098856 restraints weight = 3110.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.102554 restraints weight = 1594.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.105043 restraints weight = 1027.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.106876 restraints weight = 737.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.108173 restraints weight = 565.236| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2052 Z= 0.114 Angle : 0.591 4.301 2592 Z= 0.296 Chirality : 0.066 0.166 324 Planarity : 0.002 0.010 252 Dihedral : 41.321 179.297 252 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.93 % Allowed : 11.57 % Favored : 87.50 % 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: 3.19 (0.56), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.44 (0.43), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE O 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 2016) covalent geometry : angle 0.59130 / 0.30 ( 2592) hydrogen bonds : bond 0.03057 / 1.93 ( 24) hydrogen bonds : angle 3.82966 / 2.45 ( 72) Misc. bond : bond 0.00013 / 0.01 ( 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 26 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.093 Fit side-chains REVERT: A 5 PHE cc_start: 0.7753 (p90) cc_final: 0.7458 (p90) REVERT: G 5 PHE cc_start: 0.7735 (p90) cc_final: 0.5365 (m-80) REVERT: J 5 PHE cc_start: 0.7516 (p90) cc_final: 0.5165 (m-80) REVERT: M 5 PHE cc_start: 0.7663 (p90) cc_final: 0.7110 (p90) REVERT: V 5 PHE cc_start: 0.7638 (p90) cc_final: 0.7404 (p90) REVERT: d 5 PHE cc_start: 0.8181 (p90) cc_final: 0.7805 (p90) REVERT: j 2 ILE cc_start: 0.8910 (tt) cc_final: 0.8627 (pt) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.0250 time to fit residues: 0.9200 Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 2 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091847 restraints weight = 3412.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095386 restraints weight = 1702.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.097869 restraints weight = 1096.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.099653 restraints weight = 791.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100967 restraints weight = 606.607| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.044 2052 Z= 0.463 Angle : 0.987 7.087 2592 Z= 0.507 Chirality : 0.076 0.175 324 Planarity : 0.004 0.015 252 Dihedral : 41.263 179.913 252 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.63 % Allowed : 15.28 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.59), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.70 (0.45), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.005 PHE T 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01185 / 0.47 ( 2016) covalent geometry : angle 0.98695 / 0.51 ( 2592) hydrogen bonds : bond 0.05237 / 3.32 ( 24) hydrogen bonds : angle 4.46358 / 2.80 ( 72) Misc. bond : bond 0.00086 / 0.06 ( 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 36 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.100 Fit side-chains REVERT: A 5 PHE cc_start: 0.7870 (p90) cc_final: 0.7499 (p90) REVERT: G 5 PHE cc_start: 0.7965 (p90) cc_final: 0.5657 (m-80) REVERT: J 5 PHE cc_start: 0.7793 (p90) cc_final: 0.5097 (m-80) REVERT: M 5 PHE cc_start: 0.8018 (p90) cc_final: 0.7419 (p90) REVERT: O 5 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8258 (p90) REVERT: P 5 PHE cc_start: 0.7744 (p90) cc_final: 0.7187 (p90) REVERT: R 1 LYS cc_start: 0.8877 (tttt) cc_final: 0.8335 (ttmt) REVERT: e 5 PHE cc_start: 0.7600 (p90) cc_final: 0.7169 (p90) REVERT: j 2 ILE cc_start: 0.8965 (tt) cc_final: 0.8503 (pt) outliers start: 10 outliers final: 7 residues processed: 32 average time/residue: 0.0549 time to fit residues: 2.1828 Evaluate side-chains 33 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain h residue 5 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.115507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.099484 restraints weight = 3192.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.103112 restraints weight = 1636.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.105592 restraints weight = 1053.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107324 restraints weight = 754.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.108367 restraints weight = 577.233| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2052 Z= 0.079 Angle : 0.474 3.295 2592 Z= 0.231 Chirality : 0.064 0.141 324 Planarity : 0.002 0.007 252 Dihedral : 41.512 179.568 252 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.17 % Allowed : 18.52 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.60), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.14 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE O 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.08 ( 2016) covalent geometry : angle 0.47381 / 0.23 ( 2592) hydrogen bonds : bond 0.01883 / 1.15 ( 24) hydrogen bonds : angle 3.96959 / 2.50 ( 72) Misc. bond : bond 0.00026 / 0.02 ( 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 36 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.060 Fit side-chains REVERT: A 5 PHE cc_start: 0.7781 (p90) cc_final: 0.7501 (p90) REVERT: D 5 PHE cc_start: 0.7839 (p90) cc_final: 0.5379 (m-80) REVERT: G 5 PHE cc_start: 0.7907 (p90) cc_final: 0.5276 (m-80) REVERT: J 5 PHE cc_start: 0.7697 (p90) cc_final: 0.4961 (m-80) REVERT: M 5 PHE cc_start: 0.7927 (p90) cc_final: 0.7102 (p90) REVERT: S 5 PHE cc_start: 0.7774 (p90) cc_final: 0.7532 (p90) REVERT: e 5 PHE cc_start: 0.6834 (p90) cc_final: 0.6471 (p90) REVERT: j 2 ILE cc_start: 0.8875 (tt) cc_final: 0.8619 (pt) REVERT: j 5 PHE cc_start: 0.8370 (p90) cc_final: 0.8140 (p90) outliers start: 9 outliers final: 3 residues processed: 34 average time/residue: 0.0245 time to fit residues: 1.1831 Evaluate side-chains 29 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain c residue 2 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.090847 restraints weight = 3505.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094341 restraints weight = 1784.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096724 restraints weight = 1151.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.098462 restraints weight = 829.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.099770 restraints weight = 636.293| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.053 2052 Z= 0.565 Angle : 1.059 6.446 2592 Z= 0.544 Chirality : 0.077 0.168 324 Planarity : 0.004 0.018 252 Dihedral : 41.448 179.867 252 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 8.33 % Allowed : 11.11 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.61), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.88 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.040 0.005 PHE Q 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01444 / 0.57 ( 2016) covalent geometry : angle 1.05910 / 0.54 ( 2592) hydrogen bonds : bond 0.05480 / 3.40 ( 24) hydrogen bonds : angle 4.83848 / 2.88 ( 72) Misc. bond : bond 0.00079 / 0.05 ( 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 48 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.052 Fit side-chains REVERT: A 5 PHE cc_start: 0.7896 (p90) cc_final: 0.7496 (p90) REVERT: G 5 PHE cc_start: 0.7963 (p90) cc_final: 0.5594 (m-80) REVERT: J 5 PHE cc_start: 0.7865 (p90) cc_final: 0.5208 (m-80) REVERT: M 5 PHE cc_start: 0.8090 (p90) cc_final: 0.7548 (p90) REVERT: P 5 PHE cc_start: 0.7717 (p90) cc_final: 0.7252 (p90) REVERT: R 1 LYS cc_start: 0.8897 (tttt) cc_final: 0.8366 (ttmt) REVERT: S 5 PHE cc_start: 0.7764 (p90) cc_final: 0.7463 (p90) REVERT: X 1 LYS cc_start: 0.8864 (tttt) cc_final: 0.8470 (ttmt) REVERT: e 5 PHE cc_start: 0.7581 (p90) cc_final: 0.7313 (p90) REVERT: j 2 ILE cc_start: 0.9116 (tt) cc_final: 0.8642 (pt) outliers start: 18 outliers final: 15 residues processed: 43 average time/residue: 0.0558 time to fit residues: 2.8579 Evaluate side-chains 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain h residue 5 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.115425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.099436 restraints weight = 3267.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.103131 restraints weight = 1628.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.105666 restraints weight = 1042.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.107437 restraints weight = 739.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.108766 restraints weight = 560.610| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2052 Z= 0.086 Angle : 0.491 3.498 2592 Z= 0.241 Chirality : 0.063 0.134 324 Planarity : 0.002 0.011 252 Dihedral : 41.644 179.606 252 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.17 % Allowed : 16.20 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.63), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.35 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.002 PHE X 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 2016) covalent geometry : angle 0.49121 / 0.24 ( 2592) hydrogen bonds : bond 0.01889 / 1.11 ( 24) hydrogen bonds : angle 3.93764 / 2.45 ( 72) Misc. bond : bond 0.00012 / 0.01 ( 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 32 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.065 Fit side-chains REVERT: A 5 PHE cc_start: 0.7704 (p90) cc_final: 0.7416 (p90) REVERT: D 5 PHE cc_start: 0.7803 (p90) cc_final: 0.5326 (m-80) REVERT: G 5 PHE cc_start: 0.7953 (p90) cc_final: 0.5527 (m-80) REVERT: J 5 PHE cc_start: 0.7742 (p90) cc_final: 0.5110 (m-80) REVERT: M 5 PHE cc_start: 0.7945 (p90) cc_final: 0.7150 (p90) REVERT: O 2 ILE cc_start: 0.9041 (pt) cc_final: 0.8804 (pt) REVERT: S 5 PHE cc_start: 0.7774 (p90) cc_final: 0.7558 (p90) REVERT: d 5 PHE cc_start: 0.8338 (p90) cc_final: 0.7917 (p90) REVERT: e 5 PHE cc_start: 0.6903 (p90) cc_final: 0.6606 (p90) REVERT: j 2 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8592 (pt) outliers start: 9 outliers final: 7 residues processed: 30 average time/residue: 0.0208 time to fit residues: 0.9516 Evaluate side-chains 31 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.107208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.091879 restraints weight = 3451.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095285 restraints weight = 1795.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097637 restraints weight = 1162.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.099306 restraints weight = 841.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.100603 restraints weight = 646.469| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.044 2052 Z= 0.475 Angle : 0.965 6.093 2592 Z= 0.490 Chirality : 0.073 0.157 324 Planarity : 0.003 0.014 252 Dihedral : 41.296 179.851 252 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 7.87 % Allowed : 12.04 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.63), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.56 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.005 PHE Q 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01219 / 0.48 ( 2016) covalent geometry : angle 0.96458 / 0.49 ( 2592) hydrogen bonds : bond 0.04981 / 3.06 ( 24) hydrogen bonds : angle 4.71567 / 2.81 ( 72) Misc. bond : bond 0.00062 / 0.04 ( 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 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.104 Fit side-chains REVERT: A 5 PHE cc_start: 0.7881 (p90) cc_final: 0.7486 (p90) REVERT: F 2 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8966 (pt) REVERT: G 5 PHE cc_start: 0.7936 (p90) cc_final: 0.5647 (m-10) REVERT: J 5 PHE cc_start: 0.7841 (p90) cc_final: 0.5295 (m-80) REVERT: M 5 PHE cc_start: 0.8038 (p90) cc_final: 0.7489 (p90) REVERT: S 5 PHE cc_start: 0.7697 (p90) cc_final: 0.7487 (p90) REVERT: X 1 LYS cc_start: 0.8905 (tttt) cc_final: 0.8531 (ttmt) REVERT: e 5 PHE cc_start: 0.7536 (p90) cc_final: 0.7291 (p90) outliers start: 17 outliers final: 12 residues processed: 40 average time/residue: 0.0385 time to fit residues: 1.9361 Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain h residue 5 PHE Chi-restraints excluded: chain j residue 2 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.116383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.100193 restraints weight = 3248.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.103700 restraints weight = 1726.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.106097 restraints weight = 1120.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.107832 restraints weight = 812.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109080 restraints weight = 629.791| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2052 Z= 0.081 Angle : 0.476 3.121 2592 Z= 0.233 Chirality : 0.063 0.139 324 Planarity : 0.002 0.012 252 Dihedral : 41.549 179.398 252 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.56 % Allowed : 14.81 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.65), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.14 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE O 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.08 ( 2016) covalent geometry : angle 0.47609 / 0.23 ( 2592) hydrogen bonds : bond 0.01668 / 1.00 ( 24) hydrogen bonds : angle 3.91160 / 2.42 ( 72) Misc. bond : bond 0.00016 / 0.01 ( 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 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.084 Fit side-chains REVERT: A 5 PHE cc_start: 0.7710 (p90) cc_final: 0.7435 (p90) REVERT: D 5 PHE cc_start: 0.7760 (p90) cc_final: 0.5376 (m-80) REVERT: F 2 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8805 (pt) REVERT: G 5 PHE cc_start: 0.7954 (p90) cc_final: 0.5567 (m-80) REVERT: J 5 PHE cc_start: 0.7764 (p90) cc_final: 0.5224 (m-80) REVERT: M 5 PHE cc_start: 0.7964 (p90) cc_final: 0.7273 (p90) REVERT: S 5 PHE cc_start: 0.7731 (p90) cc_final: 0.7528 (p90) REVERT: d 5 PHE cc_start: 0.8356 (p90) cc_final: 0.8000 (p90) REVERT: e 5 PHE cc_start: 0.6871 (p90) cc_final: 0.6590 (p90) REVERT: j 2 ILE cc_start: 0.8855 (tt) cc_final: 0.8592 (pt) outliers start: 12 outliers final: 9 residues processed: 35 average time/residue: 0.0228 time to fit residues: 1.1575 Evaluate side-chains 35 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.108220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092718 restraints weight = 3427.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096101 restraints weight = 1811.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098452 restraints weight = 1185.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100054 restraints weight = 866.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.101353 restraints weight = 673.575| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.044 2052 Z= 0.475 Angle : 0.949 5.477 2592 Z= 0.483 Chirality : 0.073 0.157 324 Planarity : 0.004 0.017 252 Dihedral : 41.233 179.836 252 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.94 % Allowed : 13.43 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.64), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.50 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.040 0.005 PHE X 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01226 / 0.48 ( 2016) covalent geometry : angle 0.94852 / 0.48 ( 2592) hydrogen bonds : bond 0.04865 / 3.02 ( 24) hydrogen bonds : angle 4.75189 / 2.81 ( 72) Misc. bond : bond 0.00060 / 0.04 ( 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 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.086 Fit side-chains REVERT: A 5 PHE cc_start: 0.7920 (p90) cc_final: 0.7521 (p90) REVERT: D 5 PHE cc_start: 0.8006 (p90) cc_final: 0.5706 (m-80) REVERT: F 2 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8943 (pt) REVERT: G 5 PHE cc_start: 0.7937 (p90) cc_final: 0.5569 (m-10) REVERT: J 5 PHE cc_start: 0.7869 (p90) cc_final: 0.5314 (m-80) REVERT: M 5 PHE cc_start: 0.8042 (p90) cc_final: 0.7544 (p90) REVERT: S 5 PHE cc_start: 0.7699 (p90) cc_final: 0.7462 (p90) REVERT: X 1 LYS cc_start: 0.8908 (tttt) cc_final: 0.8535 (ttmt) REVERT: e 5 PHE cc_start: 0.7446 (p90) cc_final: 0.7245 (p90) outliers start: 15 outliers final: 11 residues processed: 39 average time/residue: 0.0445 time to fit residues: 2.1874 Evaluate side-chains 40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.116463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.100073 restraints weight = 3391.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.103677 restraints weight = 1793.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.106057 restraints weight = 1170.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.107784 restraints weight = 847.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.108864 restraints weight = 656.977| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2052 Z= 0.083 Angle : 0.478 3.227 2592 Z= 0.234 Chirality : 0.063 0.137 324 Planarity : 0.002 0.012 252 Dihedral : 41.422 179.408 252 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.17 % Allowed : 16.20 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.67), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.10 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE O 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.08 ( 2016) covalent geometry : angle 0.47776 / 0.23 ( 2592) hydrogen bonds : bond 0.01761 / 1.07 ( 24) hydrogen bonds : angle 3.84847 / 2.37 ( 72) Misc. bond : bond 0.00014 / 0.01 ( 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 35 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.096 Fit side-chains REVERT: A 5 PHE cc_start: 0.7700 (p90) cc_final: 0.7399 (p90) REVERT: D 5 PHE cc_start: 0.7755 (p90) cc_final: 0.5399 (m-80) REVERT: G 5 PHE cc_start: 0.7937 (p90) cc_final: 0.5577 (m-80) REVERT: J 5 PHE cc_start: 0.7766 (p90) cc_final: 0.5281 (m-80) REVERT: M 5 PHE cc_start: 0.7932 (p90) cc_final: 0.7374 (p90) REVERT: e 5 PHE cc_start: 0.6824 (p90) cc_final: 0.6589 (p90) REVERT: j 2 ILE cc_start: 0.8889 (tt) cc_final: 0.8615 (pt) outliers start: 9 outliers final: 8 residues processed: 33 average time/residue: 0.0326 time to fit residues: 1.4798 Evaluate side-chains 33 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain c residue 2 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.108197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092577 restraints weight = 3482.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096007 restraints weight = 1823.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098299 restraints weight = 1193.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.099977 restraints weight = 875.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.101293 restraints weight = 675.961| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.047 2052 Z= 0.477 Angle : 0.954 5.295 2592 Z= 0.484 Chirality : 0.073 0.158 324 Planarity : 0.004 0.016 252 Dihedral : 41.160 179.790 252 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.48 % Allowed : 14.35 % Favored : 79.17 % 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: 0.56 (0.64), residues: 144 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.44 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.038 0.005 PHE O 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01232 / 0.48 ( 2016) covalent geometry : angle 0.95356 / 0.48 ( 2592) hydrogen bonds : bond 0.04863 / 3.00 ( 24) hydrogen bonds : angle 4.78332 / 2.84 ( 72) Misc. bond : bond 0.00063 / 0.04 ( 36) =============================================================================== Job complete usr+sys time: 293.40 seconds wall clock time: 5 minutes 54.40 seconds (354.40 seconds total)