Starting phenix.real_space_refine on Tue Aug 26 06:51:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpt_16785/08_2025/8cpt_16785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpt_16785/08_2025/8cpt_16785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cpt_16785/08_2025/8cpt_16785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpt_16785/08_2025/8cpt_16785.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpt_16785/08_2025/8cpt_16785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpt_16785/08_2025/8cpt_16785.cif" } resolution = 1.79 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 8530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36024 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "2" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "4" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "6" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "M" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "O" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Q" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "S" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "W" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "X" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Y" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "a" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "e" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "r" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Time building chain proxies: 8.21, per 1000 atoms: 0.23 Number of scatterers: 36024 At special positions: 0 Unit cell: (131.856, 131.856, 131.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 Mg 14 11.99 Na 24 11.00 O 8530 8.00 N 5976 7.00 C 21312 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=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 77 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 163 through 174 Processing helix chain '2' and resid 13 through 42 Processing helix chain '2' and resid 48 through 77 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 163 through 174 Processing helix chain '4' and resid 13 through 42 Processing helix chain '4' and resid 48 through 77 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 163 through 174 Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 48 through 76 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 163 through 174 Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 77 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 Processing helix chain 'a' and resid 13 through 42 Processing helix chain 'a' and resid 48 through 76 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 163 through 174 Processing helix chain 'e' and resid 13 through 42 Processing helix chain 'e' and resid 48 through 77 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 163 through 174 Processing helix chain 'r' and resid 13 through 42 Processing helix chain 'r' and resid 48 through 77 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 163 through 174 2706 hydrogen bonds defined for protein. 8118 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: 6.49 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11640 1.34 - 1.46: 5268 1.46 - 1.57: 17604 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX X 90 " pdb=" SG CSX X 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CB CSX M 90 " pdb=" SG CSX M 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CB CSX B 90 " pdb=" SG CSX B 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CB CSX S 90 " pdb=" SG CSX S 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CB CSX F 90 " pdb=" SG CSX F 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 43085 1.17 - 2.35: 2975 2.35 - 3.52: 528 3.52 - 4.70: 177 4.70 - 5.87: 83 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR H 39 " pdb=" CB TYR H 39 " pdb=" CG TYR H 39 " ideal model delta sigma weight residual 113.90 108.03 5.87 1.80e+00 3.09e-01 1.06e+01 angle pdb=" CA TYR B 39 " pdb=" CB TYR B 39 " pdb=" CG TYR B 39 " ideal model delta sigma weight residual 113.90 108.10 5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA TYR A 39 " pdb=" CB TYR A 39 " pdb=" CG TYR A 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR 4 39 " pdb=" CB TYR 4 39 " pdb=" CG TYR 4 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR 1 39 " pdb=" CB TYR 1 39 " pdb=" CG TYR 1 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 19073 17.90 - 35.79: 1436 35.79 - 53.69: 276 53.69 - 71.58: 119 71.58 - 89.48: 96 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL A 46 " pdb=" C VAL A 46 " pdb=" N ALA A 47 " pdb=" CA ALA A 47 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N ALA E 47 " pdb=" CA ALA E 47 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL M 46 " pdb=" C VAL M 46 " pdb=" N ALA M 47 " pdb=" CA ALA M 47 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3523 0.047 - 0.094: 1050 0.094 - 0.141: 238 0.141 - 0.189: 67 0.189 - 0.236: 42 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR r 137 " pdb=" N TYR r 137 " pdb=" C TYR r 137 " pdb=" CB TYR r 137 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA TYR A 137 " pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CB TYR A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA TYR F 137 " pdb=" N TYR F 137 " pdb=" C TYR F 137 " pdb=" CB TYR F 137 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 137 " 0.025 2.00e-02 2.50e+03 1.82e-02 6.59e+00 pdb=" CG TYR P 137 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR P 137 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR P 137 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR P 137 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR P 137 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR P 137 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR P 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR r 137 " -0.025 2.00e-02 2.50e+03 1.81e-02 6.57e+00 pdb=" CG TYR r 137 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR r 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR r 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR r 137 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR r 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR r 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR r 137 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 137 " -0.025 2.00e-02 2.50e+03 1.81e-02 6.56e+00 pdb=" CG TYR E 137 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR E 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR E 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 137 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR E 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 137 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 137 " -0.018 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2284 2.71 - 3.25: 39076 3.25 - 3.80: 72277 3.80 - 4.35: 92805 4.35 - 4.90: 144621 Nonbonded interactions: 351063 Sorted by model distance: nonbonded pdb=" NH2 ARG S 63 " pdb=" O HOH S 601 " model vdw 2.157 3.120 nonbonded pdb=" OD1 ASP H 91 " pdb=" O HOH H 301 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP B 91 " pdb=" O HOH B 601 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP r 91 " pdb=" O HOH r 601 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP 1 91 " pdb=" O HOH 1 301 " model vdw 2.241 3.040 ... (remaining 351058 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: 0.01 Found NCS groups: ncs_group { reference = (chain '1' and resid 4 through 201) selection = (chain '2' and resid 4 through 201) selection = (chain '4' and resid 4 through 201) selection = (chain '6' and resid 4 through 201) selection = (chain 'A' and resid 4 through 500) selection = (chain 'B' and resid 4 through 500) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 4 through 201) selection = (chain 'H' and resid 4 through 201) selection = chain 'I' selection = chain 'K' selection = (chain 'M' and resid 4 through 201) selection = (chain 'O' and resid 4 through 500) selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 32.360 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.004 0.074 34776 Z= 0.208 Angle : 0.719 5.874 46848 Z= 0.413 Chirality : 0.052 0.236 4920 Planarity : 0.007 0.060 6192 Dihedral : 15.650 89.477 13032 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.49 % Allowed : 5.04 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 2.30 (0.13), residues: 4032 helix: 1.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.94 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.003 ARG K 76 TYR 0.036 0.005 TYR E 137 PHE 0.028 0.004 PHE W 41 TRP 0.012 0.003 TRP r 93 HIS 0.011 0.002 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00407 (34776) covalent geometry : angle 0.71912 (46848) hydrogen bonds : bond 0.06558 ( 2706) hydrogen bonds : angle 4.37837 ( 8118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 694 time to evaluate : 1.468 Fit side-chains REVERT: 1 124 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8042 (mmtt) REVERT: 2 124 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8047 (mmtt) REVERT: 4 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8040 (mmtt) REVERT: 6 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8027 (mmtt) REVERT: A 124 LYS cc_start: 0.8242 (mmtt) cc_final: 0.8033 (mmtt) REVERT: B 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8036 (mmtt) REVERT: E 124 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8033 (mmtt) REVERT: F 124 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8034 (mmtt) REVERT: G 124 LYS cc_start: 0.8244 (mmtt) cc_final: 0.8025 (mmtt) REVERT: H 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8034 (mmtt) REVERT: I 124 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8040 (mmtt) REVERT: K 124 LYS cc_start: 0.8247 (mmtt) cc_final: 0.8037 (mmtt) REVERT: M 70 MET cc_start: 0.9008 (mtp) cc_final: 0.8703 (mtp) REVERT: M 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8031 (mmtt) REVERT: O 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8039 (mmtt) REVERT: P 124 LYS cc_start: 0.8255 (mmtt) cc_final: 0.8043 (mmtt) REVERT: Q 124 LYS cc_start: 0.8241 (mmtt) cc_final: 0.8023 (mmtt) REVERT: S 124 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8042 (mmtt) REVERT: U 124 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8043 (mmtt) REVERT: W 124 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8032 (mmtt) REVERT: X 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8040 (mmtt) REVERT: Y 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8039 (mmtt) REVERT: a 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8030 (mmtt) REVERT: e 124 LYS cc_start: 0.8245 (mmtt) cc_final: 0.8038 (mmtt) REVERT: r 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8038 (mmtt) outliers start: 18 outliers final: 18 residues processed: 712 average time/residue: 1.1311 time to fit residues: 904.8673 Evaluate side-chains 574 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 556 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN I 136 HIS K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.142395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.138139 restraints weight = 18264.216| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 0.21 r_work: 0.3226 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 1.15 restraints_weight: 0.2500 r_work: 0.2894 rms_B_bonded: 3.27 restraints_weight: 0.1250 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34776 Z= 0.171 Angle : 0.634 6.178 46848 Z= 0.356 Chirality : 0.042 0.162 4920 Planarity : 0.004 0.027 6192 Dihedral : 5.446 46.849 4572 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.49 % Allowed : 4.90 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.02 (0.13), residues: 4032 helix: 3.04 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.83 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S 43 TYR 0.029 0.003 TYR 4 39 PHE 0.026 0.003 PHE 1 41 TRP 0.009 0.002 TRP 2 93 HIS 0.005 0.002 HIS 4 128 Details of bonding type rmsd covalent geometry : bond 0.00333 (34776) covalent geometry : angle 0.63403 (46848) hydrogen bonds : bond 0.05596 ( 2706) hydrogen bonds : angle 3.98886 ( 8118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 613 time to evaluate : 1.438 Fit side-chains REVERT: M 70 MET cc_start: 0.9139 (mtp) cc_final: 0.8884 (mtp) outliers start: 18 outliers final: 18 residues processed: 631 average time/residue: 1.1752 time to fit residues: 837.4434 Evaluate side-chains 619 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 601 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 392 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 199 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 275 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 chunk 252 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 60 HIS G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 109 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.141945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.137698 restraints weight = 18395.183| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.22 r_work: 0.3224 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 1.15 restraints_weight: 0.2500 r_work: 0.2887 rms_B_bonded: 3.30 restraints_weight: 0.1250 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 34776 Z= 0.179 Angle : 0.636 6.135 46848 Z= 0.357 Chirality : 0.041 0.166 4920 Planarity : 0.004 0.029 6192 Dihedral : 5.482 47.434 4572 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.69 % Allowed : 3.70 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.08 (0.13), residues: 4032 helix: 3.10 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.76 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG S 63 TYR 0.028 0.003 TYR H 39 PHE 0.026 0.004 PHE 1 41 TRP 0.009 0.002 TRP S 93 HIS 0.004 0.001 HIS I 128 Details of bonding type rmsd covalent geometry : bond 0.00352 (34776) covalent geometry : angle 0.63638 (46848) hydrogen bonds : bond 0.05720 ( 2706) hydrogen bonds : angle 3.99848 ( 8118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 619 time to evaluate : 1.550 Fit side-chains outliers start: 62 outliers final: 39 residues processed: 637 average time/residue: 1.1910 time to fit residues: 856.4814 Evaluate side-chains 640 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 601 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 14 GLN Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 375 optimal weight: 10.0000 chunk 358 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 390 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 326 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 60 HIS G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 109 ASN W 136 HIS X 109 ASN Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 109 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.140666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.136465 restraints weight = 18284.590| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 0.21 r_work: 0.3204 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.2872 rms_B_bonded: 3.23 restraints_weight: 0.1250 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 34776 Z= 0.235 Angle : 0.717 6.344 46848 Z= 0.404 Chirality : 0.044 0.172 4920 Planarity : 0.005 0.036 6192 Dihedral : 5.556 48.296 4572 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.90 % Allowed : 4.68 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 3.58 (0.13), residues: 4032 helix: 2.73 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.69 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 43 TYR 0.031 0.004 TYR I 39 PHE 0.030 0.005 PHE O 41 TRP 0.011 0.003 TRP a 93 HIS 0.005 0.002 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00470 (34776) covalent geometry : angle 0.71690 (46848) hydrogen bonds : bond 0.06333 ( 2706) hydrogen bonds : angle 4.18072 ( 8118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 607 time to evaluate : 1.659 Fit side-chains outliers start: 33 outliers final: 28 residues processed: 627 average time/residue: 1.2101 time to fit residues: 856.2676 Evaluate side-chains 629 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 601 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 284 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 370 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 136 HIS 2 109 ASN 2 136 HIS 4 109 ASN 4 136 HIS 6 109 ASN 6 136 HIS A 109 ASN A 136 HIS B 109 ASN B 136 HIS E 109 ASN F 109 ASN G 60 HIS G 109 ASN G 136 HIS H 109 ASN H 136 HIS I 109 ASN K 109 ASN K 136 HIS M 109 ASN M 136 HIS O 109 ASN O 136 HIS P 60 HIS P 109 ASN P 136 HIS Q 60 HIS Q 109 ASN Q 136 HIS S 60 HIS S 109 ASN S 136 HIS U 60 HIS U 109 ASN U 136 HIS W 109 ASN X 109 ASN X 136 HIS Y 109 ASN Y 136 HIS a 60 HIS a 109 ASN a 136 HIS e 60 HIS e 109 ASN e 136 HIS r 109 ASN r 136 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.143529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.139380 restraints weight = 18273.715| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.21 r_work: 0.3244 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2910 rms_B_bonded: 3.31 restraints_weight: 0.1250 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34776 Z= 0.151 Angle : 0.579 5.731 46848 Z= 0.325 Chirality : 0.039 0.148 4920 Planarity : 0.003 0.022 6192 Dihedral : 5.446 46.914 4572 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.29 % Allowed : 3.89 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.21 (0.13), residues: 4032 helix: 3.21 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.72 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 63 TYR 0.026 0.003 TYR 1 39 PHE 0.022 0.003 PHE A 41 TRP 0.010 0.002 TRP 6 93 HIS 0.003 0.001 HIS Y 128 Details of bonding type rmsd covalent geometry : bond 0.00291 (34776) covalent geometry : angle 0.57927 (46848) hydrogen bonds : bond 0.05319 ( 2706) hydrogen bonds : angle 3.87136 ( 8118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 609 time to evaluate : 1.558 Fit side-chains outliers start: 84 outliers final: 64 residues processed: 633 average time/residue: 1.1971 time to fit residues: 854.7803 Evaluate side-chains 665 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 601 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 14 GLN Chi-restraints excluded: chain r residue 53 LYS Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 35 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 chunk 203 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 214 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN F 136 HIS G 60 HIS G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 109 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.141231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.137005 restraints weight = 18303.904| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.21 r_work: 0.3210 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work: 0.2879 rms_B_bonded: 3.25 restraints_weight: 0.1250 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 34776 Z= 0.218 Angle : 0.688 6.204 46848 Z= 0.387 Chirality : 0.043 0.169 4920 Planarity : 0.005 0.033 6192 Dihedral : 5.541 48.121 4572 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.20 % Allowed : 4.28 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 3.74 (0.13), residues: 4032 helix: 2.86 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.66 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 43 TYR 0.030 0.004 TYR H 39 PHE 0.027 0.004 PHE r 41 TRP 0.011 0.003 TRP 6 93 HIS 0.005 0.002 HIS 2 57 Details of bonding type rmsd covalent geometry : bond 0.00435 (34776) covalent geometry : angle 0.68791 (46848) hydrogen bonds : bond 0.06176 ( 2706) hydrogen bonds : angle 4.11415 ( 8118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 608 time to evaluate : 1.550 Fit side-chains outliers start: 44 outliers final: 44 residues processed: 632 average time/residue: 1.1389 time to fit residues: 811.1898 Evaluate side-chains 645 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 601 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 53 LYS Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 204 optimal weight: 7.9990 chunk 315 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 357 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 373 optimal weight: 0.8980 chunk 376 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN E 136 HIS F 109 ASN G 60 HIS G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 109 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.145632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.141472 restraints weight = 18302.193| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 0.21 r_work: 0.3275 rms_B_bonded: 0.56 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work: 0.2941 rms_B_bonded: 3.32 restraints_weight: 0.1250 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 34776 Z= 0.124 Angle : 0.529 5.387 46848 Z= 0.295 Chirality : 0.037 0.145 4920 Planarity : 0.003 0.020 6192 Dihedral : 5.343 45.728 4572 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.93 % Allowed : 4.08 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.52 (0.13), residues: 4032 helix: 3.46 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.63 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 63 TYR 0.023 0.002 TYR H 39 PHE 0.018 0.002 PHE 4 41 TRP 0.010 0.002 TRP 6 93 HIS 0.003 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00231 (34776) covalent geometry : angle 0.52942 (46848) hydrogen bonds : bond 0.04816 ( 2706) hydrogen bonds : angle 3.72024 ( 8118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 623 time to evaluate : 1.525 Fit side-chains outliers start: 71 outliers final: 44 residues processed: 647 average time/residue: 1.0289 time to fit residues: 754.0705 Evaluate side-chains 640 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 596 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 397 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.141222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.136995 restraints weight = 18146.162| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 0.22 r_work: 0.3215 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.2883 rms_B_bonded: 3.22 restraints_weight: 0.1250 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 34776 Z= 0.232 Angle : 0.705 6.168 46848 Z= 0.397 Chirality : 0.043 0.167 4920 Planarity : 0.005 0.035 6192 Dihedral : 5.536 48.347 4572 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.33 % Allowed : 5.07 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 3.78 (0.13), residues: 4032 helix: 2.90 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.61 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 43 TYR 0.033 0.004 TYR H 39 PHE 0.028 0.005 PHE a 41 TRP 0.010 0.003 TRP 2 93 HIS 0.005 0.002 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00464 (34776) covalent geometry : angle 0.70507 (46848) hydrogen bonds : bond 0.06263 ( 2706) hydrogen bonds : angle 4.13163 ( 8118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 606 time to evaluate : 1.284 Fit side-chains outliers start: 49 outliers final: 48 residues processed: 630 average time/residue: 1.0484 time to fit residues: 748.0923 Evaluate side-chains 629 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 581 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 110 optimal weight: 2.9990 chunk 399 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 391 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 348 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.143362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.139210 restraints weight = 18054.247| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 0.21 r_work: 0.3245 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2911 rms_B_bonded: 3.22 restraints_weight: 0.1250 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34776 Z= 0.162 Angle : 0.600 5.803 46848 Z= 0.336 Chirality : 0.039 0.152 4920 Planarity : 0.004 0.024 6192 Dihedral : 5.473 47.357 4572 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.28 % Allowed : 5.15 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.15 (0.13), residues: 4032 helix: 3.17 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.66 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 43 TYR 0.027 0.003 TYR H 39 PHE 0.024 0.003 PHE X 41 TRP 0.011 0.002 TRP 6 93 HIS 0.003 0.001 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00316 (34776) covalent geometry : angle 0.60032 (46848) hydrogen bonds : bond 0.05462 ( 2706) hydrogen bonds : angle 3.90203 ( 8118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 596 time to evaluate : 1.557 Fit side-chains outliers start: 47 outliers final: 47 residues processed: 620 average time/residue: 1.1520 time to fit residues: 808.9944 Evaluate side-chains 619 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 572 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 289 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 263 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 309 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 407 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.143281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.139093 restraints weight = 18095.752| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.21 r_work: 0.3244 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 1.15 restraints_weight: 0.2500 r_work: 0.2910 rms_B_bonded: 3.24 restraints_weight: 0.1250 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34776 Z= 0.164 Angle : 0.605 5.844 46848 Z= 0.339 Chirality : 0.039 0.153 4920 Planarity : 0.004 0.024 6192 Dihedral : 5.466 47.240 4572 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.28 % Allowed : 5.15 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.15 (0.13), residues: 4032 helix: 3.17 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.65 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 43 TYR 0.028 0.003 TYR H 39 PHE 0.024 0.003 PHE E 41 TRP 0.011 0.002 TRP 6 93 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00320 (34776) covalent geometry : angle 0.60517 (46848) hydrogen bonds : bond 0.05510 ( 2706) hydrogen bonds : angle 3.90537 ( 8118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 596 time to evaluate : 1.561 Fit side-chains outliers start: 47 outliers final: 47 residues processed: 620 average time/residue: 1.1830 time to fit residues: 832.9266 Evaluate side-chains 619 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 572 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 220 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 270 optimal weight: 5.9990 chunk 396 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.141905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.137693 restraints weight = 18108.921| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 0.21 r_work: 0.3224 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.2891 rms_B_bonded: 3.20 restraints_weight: 0.1250 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 34776 Z= 0.206 Angle : 0.674 6.102 46848 Z= 0.379 Chirality : 0.042 0.167 4920 Planarity : 0.004 0.031 6192 Dihedral : 5.518 47.829 4572 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.28 % Allowed : 5.15 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 3.83 (0.13), residues: 4032 helix: 2.93 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.62 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 43 TYR 0.032 0.003 TYR H 39 PHE 0.028 0.004 PHE S 41 TRP 0.011 0.003 TRP 6 93 HIS 0.005 0.002 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00411 (34776) covalent geometry : angle 0.67369 (46848) hydrogen bonds : bond 0.06027 ( 2706) hydrogen bonds : angle 4.06201 ( 8118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21663.16 seconds wall clock time: 368 minutes 46.23 seconds (22126.23 seconds total)