Starting phenix.real_space_refine on Tue Aug 26 06:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpw_16788/08_2025/8cpw_16788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpw_16788/08_2025/8cpw_16788.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/8cpw_16788/08_2025/8cpw_16788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpw_16788/08_2025/8cpw_16788.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpw_16788/08_2025/8cpw_16788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpw_16788/08_2025/8cpw_16788.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 8510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.02s 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: 36004 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "2" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "4" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "6" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} 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: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "H" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "O" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "U" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "W" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "X" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "Y" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "a" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "e" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "r" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Time building chain proxies: 7.59, per 1000 atoms: 0.21 Number of scatterers: 36004 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 8510 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: 2.98 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 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: 0.83 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: 5.88 Time building geometry restraints manager: 3.66 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: 11624 1.34 - 1.46: 4988 1.46 - 1.57: 17900 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.755 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" CB CSX G 90 " pdb=" SG CSX G 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX Q 90 " pdb=" SG CSX Q 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CB CSX K 90 " pdb=" SG CSX K 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 42306 1.33 - 2.66: 3801 2.66 - 3.99: 563 3.99 - 5.32: 130 5.32 - 6.65: 48 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR E 39 " pdb=" CB TYR E 39 " pdb=" CG TYR E 39 " ideal model delta sigma weight residual 113.90 108.14 5.76 1.80e+00 3.09e-01 1.02e+01 angle pdb=" CA TYR I 39 " pdb=" CB TYR I 39 " pdb=" CG TYR I 39 " ideal model delta sigma weight residual 113.90 108.16 5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" CA TYR 2 39 " pdb=" CB TYR 2 39 " pdb=" CG TYR 2 39 " ideal model delta sigma weight residual 113.90 108.18 5.72 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 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR M 39 " pdb=" CB TYR M 39 " pdb=" CG TYR M 39 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 18967 16.52 - 33.04: 1481 33.04 - 49.55: 347 49.55 - 66.07: 96 66.07 - 82.59: 109 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL U 46 " pdb=" C VAL U 46 " pdb=" N ALA U 47 " pdb=" CA ALA U 47 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+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 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3454 0.056 - 0.112: 1163 0.112 - 0.168: 212 0.168 - 0.225: 68 0.225 - 0.281: 23 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR I 137 " pdb=" N TYR I 137 " pdb=" C TYR I 137 " pdb=" CB TYR I 137 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA TYR O 137 " pdb=" N TYR O 137 " pdb=" C TYR O 137 " pdb=" CB TYR O 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR E 137 " pdb=" N TYR E 137 " pdb=" C TYR E 137 " pdb=" CB TYR E 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 137 " -0.023 2.00e-02 2.50e+03 1.69e-02 5.69e+00 pdb=" CG TYR 2 137 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 137 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 137 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 137 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 2 137 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR 2 137 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 137 " 0.023 2.00e-02 2.50e+03 1.68e-02 5.66e+00 pdb=" CG TYR 1 137 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 137 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 137 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 137 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR 1 137 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR 1 137 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 137 " 0.023 2.00e-02 2.50e+03 1.68e-02 5.65e+00 pdb=" CG TYR A 137 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 137 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 137 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 137 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 137 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 137 " 0.021 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2972 2.72 - 3.27: 39534 3.27 - 3.81: 71869 3.81 - 4.36: 89786 4.36 - 4.90: 141783 Nonbonded interactions: 345944 Sorted by model distance: nonbonded pdb=" OE1 GLU M 116 " pdb=" O HOH M 301 " model vdw 2.180 3.040 nonbonded pdb=" OE1 GLU Q 116 " pdb=" O HOH Q 601 " model vdw 2.181 3.040 nonbonded pdb=" OE1 GLU W 116 " pdb=" O HOH W 601 " model vdw 2.181 3.040 nonbonded pdb=" OE1 GLU a 116 " pdb=" O HOH a 301 " model vdw 2.181 3.040 nonbonded pdb=" OE1 GLU 6 116 " pdb=" O HOH 6 301 " model vdw 2.181 3.040 ... (remaining 345939 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 176) selection = (chain '2' and resid 4 through 176) selection = (chain '4' and resid 4 through 176) selection = (chain '6' and resid 4 through 176) selection = (chain 'A' and resid 4 through 176) selection = (chain 'B' and resid 4 through 176) selection = (chain 'E' and resid 4 through 176) selection = (chain 'F' and resid 4 through 176) selection = (chain 'G' and resid 4 through 176) selection = (chain 'H' and resid 4 through 176) selection = (chain 'I' and resid 4 through 176) selection = (chain 'K' and resid 4 through 176) selection = (chain 'M' and resid 4 through 176) selection = (chain 'O' and resid 4 through 176) selection = (chain 'P' and resid 4 through 176) selection = (chain 'Q' and resid 4 through 176) selection = (chain 'S' and resid 4 through 176) selection = (chain 'U' and resid 4 through 176) selection = (chain 'W' and resid 4 through 176) selection = (chain 'X' and resid 4 through 176) selection = (chain 'Y' and resid 4 through 176) selection = (chain 'a' and resid 4 through 176) selection = (chain 'e' and resid 4 through 176) selection = (chain 'r' and resid 4 through 176) } 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.410 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 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:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.005 0.076 34776 Z= 0.256 Angle : 0.840 6.653 46848 Z= 0.483 Chirality : 0.060 0.281 4920 Planarity : 0.008 0.059 6192 Dihedral : 14.346 82.591 13032 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.63 % Allowed : 2.18 % Favored : 97.19 % 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: 2.13 (0.13), residues: 4032 helix: 1.61 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.83 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG H 76 TYR 0.029 0.006 TYR 1 137 PHE 0.028 0.006 PHE K 41 TRP 0.016 0.004 TRP e 93 HIS 0.011 0.004 HIS U 136 Details of bonding type rmsd covalent geometry : bond 0.00522 (34776) covalent geometry : angle 0.84008 (46848) hydrogen bonds : bond 0.08770 ( 2706) hydrogen bonds : angle 4.50203 ( 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 583 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 560 time to evaluate : 1.317 Fit side-chains REVERT: 2 70 MET cc_start: 0.8657 (mtp) cc_final: 0.8362 (mtp) REVERT: S 70 MET cc_start: 0.8657 (mtp) cc_final: 0.8360 (mtp) REVERT: W 70 MET cc_start: 0.8664 (mtp) cc_final: 0.8317 (mtp) REVERT: a 70 MET cc_start: 0.8668 (mtp) cc_final: 0.8323 (mtp) outliers start: 23 outliers final: 23 residues processed: 560 average time/residue: 0.9116 time to fit residues: 588.4254 Evaluate side-chains 569 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 546 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 14 GLN 4 112 GLN 6 14 GLN 6 112 GLN A 112 GLN B 14 GLN B 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 112 GLN H 14 GLN K 14 GLN K 112 GLN M 14 GLN M 112 GLN O 112 GLN P 112 GLN Q 14 GLN Q 112 GLN S 14 GLN S 112 GLN U 14 GLN U 112 GLN U 125 ASN W 14 GLN W 112 GLN X 14 GLN X 112 GLN Y 14 GLN Y 112 GLN a 14 GLN a 112 GLN a 125 ASN e 112 GLN e 125 ASN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.155605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.143766 restraints weight = 200077.522| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.77 r_work: 0.2794 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 34776 Z= 0.134 Angle : 0.564 5.695 46848 Z= 0.315 Chirality : 0.039 0.152 4920 Planarity : 0.003 0.033 6192 Dihedral : 5.682 40.795 4582 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.22 % 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: 4.45 (0.13), residues: 4032 helix: 3.38 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.85 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 63 TYR 0.021 0.002 TYR Y 39 PHE 0.017 0.003 PHE 4 41 TRP 0.011 0.002 TRP F 93 HIS 0.005 0.002 HIS O 65 Details of bonding type rmsd covalent geometry : bond 0.00251 (34776) covalent geometry : angle 0.56431 (46848) hydrogen bonds : bond 0.05381 ( 2706) hydrogen bonds : angle 3.75051 ( 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 595 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 594 time to evaluate : 1.338 Fit side-chains REVERT: 4 63 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7966 (tpt-90) REVERT: O 63 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7951 (tpt-90) REVERT: Q 63 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7960 (tpt-90) REVERT: S 70 MET cc_start: 0.8873 (mtp) cc_final: 0.8465 (mtp) REVERT: W 70 MET cc_start: 0.8878 (mtp) cc_final: 0.8497 (mtp) REVERT: X 63 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7953 (tpt-90) outliers start: 1 outliers final: 1 residues processed: 594 average time/residue: 0.8953 time to fit residues: 615.7854 Evaluate side-chains 562 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 561 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 386 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 112 GLN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 112 GLN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.154024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.142298 restraints weight = 202196.808| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.78 r_work: 0.2773 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34776 Z= 0.153 Angle : 0.609 6.572 46848 Z= 0.339 Chirality : 0.040 0.147 4920 Planarity : 0.004 0.063 6192 Dihedral : 4.497 18.784 4536 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.96 % Favored : 97.39 % 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: 4.50 (0.13), residues: 4032 helix: 3.42 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.85 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 63 TYR 0.022 0.002 TYR M 39 PHE 0.019 0.003 PHE E 41 TRP 0.011 0.003 TRP O 93 HIS 0.006 0.002 HIS X 60 Details of bonding type rmsd covalent geometry : bond 0.00298 (34776) covalent geometry : angle 0.60938 (46848) hydrogen bonds : bond 0.05836 ( 2706) hydrogen bonds : angle 3.83197 ( 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 596 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 572 time to evaluate : 1.563 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 572 average time/residue: 1.0016 time to fit residues: 662.0928 Evaluate side-chains 572 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 548 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 361 optimal weight: 0.9990 chunk 308 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 373 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 241 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 112 GLN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.154082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.142593 restraints weight = 201693.279| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.77 r_work: 0.2776 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0865 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= 0.156 Angle : 0.616 6.612 46848 Z= 0.342 Chirality : 0.040 0.157 4920 Planarity : 0.004 0.073 6192 Dihedral : 4.491 18.312 4536 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.99 % Favored : 97.36 % 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: 4.46 (0.13), residues: 4032 helix: 3.38 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.90 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG e 63 TYR 0.024 0.002 TYR 6 39 PHE 0.020 0.003 PHE 6 41 TRP 0.011 0.003 TRP X 93 HIS 0.005 0.002 HIS F 136 Details of bonding type rmsd covalent geometry : bond 0.00306 (34776) covalent geometry : angle 0.61588 (46848) hydrogen bonds : bond 0.05870 ( 2706) hydrogen bonds : angle 3.81704 ( 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 610 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 586 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 70 MET cc_start: 0.8876 (mtp) cc_final: 0.8615 (mtp) outliers start: 24 outliers final: 24 residues processed: 586 average time/residue: 0.9996 time to fit residues: 675.9319 Evaluate side-chains 583 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 559 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 51 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 161 optimal weight: 0.0770 chunk 312 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 overall best weight: 3.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.153666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.142022 restraints weight = 202035.168| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.80 r_work: 0.2766 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34776 Z= 0.173 Angle : 0.648 6.959 46848 Z= 0.359 Chirality : 0.041 0.146 4920 Planarity : 0.004 0.064 6192 Dihedral : 4.516 17.704 4536 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.59 % Favored : 96.76 % 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: 4.38 (0.13), residues: 4032 helix: 3.32 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.89 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 63 TYR 0.025 0.002 TYR B 39 PHE 0.021 0.003 PHE X 41 TRP 0.012 0.003 TRP X 93 HIS 0.006 0.002 HIS P 136 Details of bonding type rmsd covalent geometry : bond 0.00345 (34776) covalent geometry : angle 0.64835 (46848) hydrogen bonds : bond 0.06150 ( 2706) hydrogen bonds : angle 3.87816 ( 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 598 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 574 time to evaluate : 1.596 Fit side-chains REVERT: 2 63 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7944 (tpt-90) outliers start: 24 outliers final: 24 residues processed: 574 average time/residue: 1.0136 time to fit residues: 671.0144 Evaluate side-chains 575 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 551 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 368 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 401 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 320 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.152939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.141225 restraints weight = 200069.210| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.77 r_work: 0.2757 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34776 Z= 0.199 Angle : 0.694 7.170 46848 Z= 0.384 Chirality : 0.042 0.148 4920 Planarity : 0.004 0.046 6192 Dihedral : 4.558 17.080 4536 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.64 % Favored : 96.70 % 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: 4.25 (0.13), residues: 4032 helix: 3.23 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.84 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 63 TYR 0.028 0.003 TYR I 39 PHE 0.024 0.004 PHE a 41 TRP 0.011 0.003 TRP X 93 HIS 0.007 0.002 HIS F 136 Details of bonding type rmsd covalent geometry : bond 0.00405 (34776) covalent geometry : angle 0.69445 (46848) hydrogen bonds : bond 0.06464 ( 2706) hydrogen bonds : angle 3.95847 ( 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 589 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 565 time to evaluate : 1.535 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 565 average time/residue: 1.0222 time to fit residues: 664.5667 Evaluate side-chains 564 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 540 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 0 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 360 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.153650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.142023 restraints weight = 200573.107| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.74 r_work: 0.2772 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0912 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= 0.172 Angle : 0.646 6.992 46848 Z= 0.357 Chirality : 0.041 0.145 4920 Planarity : 0.004 0.030 6192 Dihedral : 4.531 17.629 4536 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.67 % Favored : 96.68 % 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: 4.37 (0.13), residues: 4032 helix: 3.33 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.79 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 63 TYR 0.023 0.002 TYR 6 39 PHE 0.021 0.003 PHE W 41 TRP 0.011 0.003 TRP Y 93 HIS 0.005 0.002 HIS I 136 Details of bonding type rmsd covalent geometry : bond 0.00341 (34776) covalent geometry : angle 0.64635 (46848) hydrogen bonds : bond 0.06079 ( 2706) hydrogen bonds : angle 3.86832 ( 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 568 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 544 time to evaluate : 1.582 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 544 average time/residue: 0.9949 time to fit residues: 621.6070 Evaluate side-chains 566 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 542 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 113 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 260 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.153135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.141515 restraints weight = 203256.071| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.76 r_work: 0.2761 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 34776 Z= 0.189 Angle : 0.680 7.113 46848 Z= 0.375 Chirality : 0.042 0.147 4920 Planarity : 0.004 0.042 6192 Dihedral : 4.555 17.079 4536 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.70 % Favored : 96.65 % 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: 4.26 (0.13), residues: 4032 helix: 3.24 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.80 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 63 TYR 0.026 0.003 TYR 6 39 PHE 0.024 0.004 PHE X 41 TRP 0.011 0.003 TRP X 93 HIS 0.006 0.002 HIS 6 136 Details of bonding type rmsd covalent geometry : bond 0.00382 (34776) covalent geometry : angle 0.68015 (46848) hydrogen bonds : bond 0.06325 ( 2706) hydrogen bonds : angle 3.93598 ( 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 580 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 556 time to evaluate : 1.418 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 556 average time/residue: 0.9067 time to fit residues: 581.1677 Evaluate side-chains 575 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 551 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 154 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 361 optimal weight: 0.3980 chunk 63 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 276 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 308 optimal weight: 0.8980 chunk 300 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.154940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.143198 restraints weight = 200731.782| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.74 r_work: 0.2785 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34776 Z= 0.149 Angle : 0.608 6.760 46848 Z= 0.336 Chirality : 0.039 0.143 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.485 17.994 4536 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.67 % Favored : 96.68 % 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: 4.48 (0.13), residues: 4032 helix: 3.42 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.79 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 63 TYR 0.022 0.002 TYR 6 39 PHE 0.020 0.003 PHE A 41 TRP 0.012 0.003 TRP Y 93 HIS 0.004 0.001 HIS H 136 Details of bonding type rmsd covalent geometry : bond 0.00289 (34776) covalent geometry : angle 0.60755 (46848) hydrogen bonds : bond 0.05728 ( 2706) hydrogen bonds : angle 3.78114 ( 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 591 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 567 time to evaluate : 1.148 Fit side-chains REVERT: 2 63 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7946 (tpt-90) outliers start: 24 outliers final: 24 residues processed: 567 average time/residue: 0.8768 time to fit residues: 573.9787 Evaluate side-chains 574 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 550 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 147 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 305 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 123 optimal weight: 0.4980 chunk 148 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 112 GLN 2 125 ASN 4 112 GLN 4 125 ASN 6 112 GLN 6 125 ASN A 112 GLN A 125 ASN B 125 ASN E 112 GLN E 125 ASN F 125 ASN G 112 GLN G 125 ASN H 125 ASN I 125 ASN K 125 ASN M 112 GLN O 125 ASN P 125 ASN Q 112 GLN Q 125 ASN S 125 ASN U 125 ASN W 112 GLN X 125 ASN Y 125 ASN a 112 GLN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.153234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.141611 restraints weight = 201372.250| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.74 r_work: 0.2767 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34776 Z= 0.182 Angle : 0.673 7.191 46848 Z= 0.371 Chirality : 0.041 0.151 4920 Planarity : 0.004 0.051 6192 Dihedral : 4.551 17.355 4536 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.64 % Favored : 96.70 % 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: 4.31 (0.13), residues: 4032 helix: 3.28 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.80 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 63 TYR 0.029 0.003 TYR M 39 PHE 0.023 0.003 PHE 1 41 TRP 0.012 0.003 TRP O 93 HIS 0.008 0.002 HIS 2 60 Details of bonding type rmsd covalent geometry : bond 0.00366 (34776) covalent geometry : angle 0.67285 (46848) hydrogen bonds : bond 0.06247 ( 2706) hydrogen bonds : angle 3.91234 ( 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 582 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 558 time to evaluate : 1.729 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 558 average time/residue: 0.9814 time to fit residues: 629.2985 Evaluate side-chains 577 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 553 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 95 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 313 optimal weight: 7.9990 chunk 336 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 347 optimal weight: 0.8980 chunk 387 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 1 125 ASN 2 125 ASN 4 125 ASN A 125 ASN B 112 GLN B 125 ASN E 125 ASN F 112 GLN F 125 ASN G 125 ASN H 112 GLN H 125 ASN I 112 GLN I 125 ASN K 112 GLN K 125 ASN O 112 GLN O 125 ASN P 112 GLN P 125 ASN Q 125 ASN S 112 GLN S 125 ASN U 112 GLN U 125 ASN X 112 GLN X 125 ASN Y 112 GLN Y 125 ASN a 125 ASN e 112 GLN e 125 ASN r 112 GLN r 125 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.155992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.144198 restraints weight = 198913.327| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.75 r_work: 0.2804 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 34776 Z= 0.132 Angle : 0.577 6.594 46848 Z= 0.318 Chirality : 0.038 0.141 4920 Planarity : 0.003 0.046 6192 Dihedral : 4.434 18.435 4536 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.67 % Favored : 96.68 % 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: 4.65 (0.13), residues: 4032 helix: 3.54 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.82 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 2 63 TYR 0.023 0.002 TYR 6 39 PHE 0.017 0.002 PHE B 41 TRP 0.012 0.003 TRP Y 93 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00246 (34776) covalent geometry : angle 0.57676 (46848) hydrogen bonds : bond 0.05391 ( 2706) hydrogen bonds : angle 3.68374 ( 8118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18078.99 seconds wall clock time: 308 minutes 27.18 seconds (18507.18 seconds total)