Starting phenix.real_space_refine on Tue Aug 26 06:36:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpx_16789/08_2025/8cpx_16789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpx_16789/08_2025/8cpx_16789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cpx_16789/08_2025/8cpx_16789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpx_16789/08_2025/8cpx_16789.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpx_16789/08_2025/8cpx_16789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpx_16789/08_2025/8cpx_16789.cif" } resolution = 1.76 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 8333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35827 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "2" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "4" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "6" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "P" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "Q" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "S" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "U" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "W" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "Y" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "a" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "e" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "r" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 9.22, per 1000 atoms: 0.26 Number of scatterers: 35827 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 8333 8.00 N 5976 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 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 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 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 77 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 77 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 77 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 77 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 77 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 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 '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 2712 hydrogen bonds defined for protein. 8136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 3.95 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: 11664 1.34 - 1.46: 6516 1.46 - 1.58: 16332 1.58 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX U 90 " pdb=" SG CSX U 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CB CSX r 90 " pdb=" SG CSX r 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CB CSX W 90 " pdb=" SG CSX W 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 43213 1.32 - 2.64: 2906 2.64 - 3.97: 521 3.97 - 5.29: 132 5.29 - 6.61: 76 Bond angle restraints: 46848 Sorted by residual: angle pdb=" C TYR I 32 " pdb=" CA TYR I 32 " pdb=" CB TYR I 32 " ideal model delta sigma weight residual 110.85 117.16 -6.31 1.70e+00 3.46e-01 1.38e+01 angle pdb=" C TYR O 32 " pdb=" CA TYR O 32 " pdb=" CB TYR O 32 " ideal model delta sigma weight residual 110.85 117.14 -6.29 1.70e+00 3.46e-01 1.37e+01 angle pdb=" C TYR U 32 " pdb=" CA TYR U 32 " pdb=" CB TYR U 32 " ideal model delta sigma weight residual 110.85 117.13 -6.28 1.70e+00 3.46e-01 1.37e+01 angle pdb=" C TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta sigma weight residual 110.85 117.13 -6.28 1.70e+00 3.46e-01 1.36e+01 angle pdb=" C TYR E 32 " pdb=" CA TYR E 32 " pdb=" CB TYR E 32 " ideal model delta sigma weight residual 110.85 117.12 -6.27 1.70e+00 3.46e-01 1.36e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 18987 16.54 - 33.08: 1440 33.08 - 49.62: 327 49.62 - 66.17: 102 66.17 - 82.71: 144 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: 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 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA VAL F 46 " pdb=" C VAL F 46 " pdb=" N ALA F 47 " pdb=" CA ALA F 47 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.14e+01 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 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3646 0.049 - 0.098: 892 0.098 - 0.147: 244 0.147 - 0.196: 86 0.196 - 0.246: 52 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CG LEU S 72 " pdb=" CB LEU S 72 " pdb=" CD1 LEU S 72 " pdb=" CD2 LEU S 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU B 72 " pdb=" CB LEU B 72 " pdb=" CD1 LEU B 72 " pdb=" CD2 LEU B 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU Y 72 " pdb=" CB LEU Y 72 " pdb=" CD1 LEU Y 72 " pdb=" CD2 LEU Y 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " -0.050 2.00e-02 2.50e+03 4.74e-02 4.49e+01 pdb=" CG TYR F 32 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 32 " 0.051 2.00e-02 2.50e+03 4.74e-02 4.48e+01 pdb=" CG TYR E 32 " -0.116 2.00e-02 2.50e+03 pdb=" CD1 TYR E 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR E 32 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR E 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR E 32 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 32 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 32 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 32 " 0.050 2.00e-02 2.50e+03 4.72e-02 4.46e+01 pdb=" CG TYR 6 32 " -0.116 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 32 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 32 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 32 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR 6 32 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR 6 32 " 0.000 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1255 2.63 - 3.20: 34663 3.20 - 3.77: 68210 3.77 - 4.33: 94117 4.33 - 4.90: 146953 Nonbonded interactions: 345198 Sorted by model distance: nonbonded pdb=" O HOH 1 301 " pdb=" O HOH 1 302 " model vdw 2.063 3.040 nonbonded pdb=" O HOH W 601 " pdb=" O HOH W 602 " model vdw 2.065 3.040 nonbonded pdb=" O HOH Q 601 " pdb=" O HOH Q 602 " model vdw 2.065 3.040 nonbonded pdb=" NZ LYS A 119 " pdb=" OD1 ASP A 123 " model vdw 2.182 3.120 nonbonded pdb=" NZ LYS P 119 " pdb=" OD1 ASP P 123 " model vdw 2.199 3.120 ... (remaining 345193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain '1' and resid 4 through 201) selection = (chain '2' and resid 4 through 201) selection = (chain '4' and resid 4 through 201) selection = (chain '6' and resid 4 through 201) selection = (chain 'A' and resid 4 through 500) selection = (chain 'B' and resid 4 through 500) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 4 through 201) selection = (chain 'H' and resid 4 through 201) selection = chain 'I' selection = chain 'K' selection = (chain 'M' and resid 4 through 201) selection = (chain 'O' and resid 4 through 500) selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.300 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 0.072 34776 Z= 0.244 Angle : 0.803 6.612 46848 Z= 0.453 Chirality : 0.056 0.246 4920 Planarity : 0.008 0.060 6192 Dihedral : 14.967 82.707 13032 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.18 (0.13), residues: 4032 helix: 1.63 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.93 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.004 ARG P 63 TYR 0.117 0.008 TYR F 32 PHE 0.028 0.005 PHE G 41 TRP 0.017 0.004 TRP H 93 HIS 0.011 0.004 HIS 1 151 Details of bonding type rmsd covalent geometry : bond 0.00492 (34776) covalent geometry : angle 0.80295 (46848) hydrogen bonds : bond 0.07434 ( 2712) hydrogen bonds : angle 4.49585 ( 8136) *********************** 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 732 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 732 time to evaluate : 1.568 Fit side-chains REVERT: 6 135 THR cc_start: 0.8317 (m) cc_final: 0.7976 (p) REVERT: G 135 THR cc_start: 0.8331 (m) cc_final: 0.7994 (p) REVERT: I 135 THR cc_start: 0.8241 (m) cc_final: 0.7962 (p) REVERT: M 135 THR cc_start: 0.8324 (m) cc_final: 0.7986 (p) REVERT: Q 135 THR cc_start: 0.8319 (m) cc_final: 0.7972 (p) REVERT: W 135 THR cc_start: 0.8324 (m) cc_final: 0.7980 (p) REVERT: a 135 THR cc_start: 0.8312 (m) cc_final: 0.7981 (p) outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.9046 time to fit residues: 765.8829 Evaluate side-chains 513 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 1 112 GLN 2 14 GLN 2 112 GLN 4 14 GLN 4 112 GLN 6 14 GLN A 14 GLN A 112 GLN B 14 GLN B 75 GLN B 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 14 GLN H 14 GLN H 112 GLN I 14 GLN I 112 GLN K 14 GLN K 112 GLN M 14 GLN O 14 GLN O 112 GLN P 14 GLN P 112 GLN Q 14 GLN S 14 GLN S 112 GLN U 14 GLN U 112 GLN W 14 GLN X 14 GLN X 112 GLN Y 14 GLN Y 112 GLN a 14 GLN e 14 GLN e 112 GLN r 14 GLN r 112 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.151214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.139561 restraints weight = 201506.988| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.78 r_work: 0.2806 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 0.021 34776 Z= 0.172 Angle : 0.657 6.313 46848 Z= 0.362 Chirality : 0.041 0.170 4920 Planarity : 0.005 0.056 6192 Dihedral : 4.624 19.915 4536 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.66 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.90 (0.13), residues: 4032 helix: 2.90 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.06 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 1 63 TYR 0.054 0.004 TYR B 32 PHE 0.019 0.004 PHE W 41 TRP 0.013 0.003 TRP a 93 HIS 0.005 0.002 HIS 6 60 Details of bonding type rmsd covalent geometry : bond 0.00345 (34776) covalent geometry : angle 0.65711 (46848) hydrogen bonds : bond 0.06134 ( 2712) hydrogen bonds : angle 3.98214 ( 8136) *********************** 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 589 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 565 time to evaluate : 1.617 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 588 average time/residue: 0.9624 time to fit residues: 651.7616 Evaluate side-chains 609 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 585 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 386 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.150691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.139258 restraints weight = 202676.315| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.77 r_work: 0.2791 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34776 Z= 0.189 Angle : 0.679 6.338 46848 Z= 0.372 Chirality : 0.041 0.167 4920 Planarity : 0.005 0.068 6192 Dihedral : 4.568 19.878 4536 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.71 % Allowed : 2.04 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.93 (0.13), residues: 4032 helix: 2.91 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.17 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG r 63 TYR 0.032 0.004 TYR A 32 PHE 0.021 0.004 PHE S 81 TRP 0.012 0.003 TRP G 93 HIS 0.006 0.002 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00386 (34776) covalent geometry : angle 0.67932 (46848) hydrogen bonds : bond 0.06405 ( 2712) hydrogen bonds : angle 4.06501 ( 8136) *********************** 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 623 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 597 time to evaluate : 1.380 Fit side-chains REVERT: 1 135 THR cc_start: 0.8614 (m) cc_final: 0.8316 (p) REVERT: 2 135 THR cc_start: 0.8598 (m) cc_final: 0.8310 (p) REVERT: 4 135 THR cc_start: 0.8611 (m) cc_final: 0.8324 (p) REVERT: A 135 THR cc_start: 0.8607 (m) cc_final: 0.8318 (p) REVERT: B 135 THR cc_start: 0.8608 (m) cc_final: 0.8323 (p) REVERT: E 135 THR cc_start: 0.8611 (m) cc_final: 0.8323 (p) REVERT: F 135 THR cc_start: 0.8609 (m) cc_final: 0.8321 (p) REVERT: H 135 THR cc_start: 0.8602 (m) cc_final: 0.8313 (p) REVERT: K 135 THR cc_start: 0.8611 (m) cc_final: 0.8322 (p) REVERT: O 135 THR cc_start: 0.8611 (m) cc_final: 0.8310 (p) REVERT: P 135 THR cc_start: 0.8607 (m) cc_final: 0.8319 (p) REVERT: S 135 THR cc_start: 0.8604 (m) cc_final: 0.8316 (p) REVERT: U 135 THR cc_start: 0.8611 (m) cc_final: 0.8325 (p) REVERT: X 135 THR cc_start: 0.8606 (m) cc_final: 0.8318 (p) REVERT: Y 135 THR cc_start: 0.8605 (m) cc_final: 0.8315 (p) REVERT: e 135 THR cc_start: 0.8615 (m) cc_final: 0.8326 (p) REVERT: r 135 THR cc_start: 0.8610 (m) cc_final: 0.8310 (p) outliers start: 26 outliers final: 24 residues processed: 615 average time/residue: 0.9895 time to fit residues: 700.3351 Evaluate side-chains 559 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 535 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS 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: 3.9990 chunk 75 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 350 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.152256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.141038 restraints weight = 200410.697| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.78 r_work: 0.2815 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1064 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= 0.150 Angle : 0.604 6.065 46848 Z= 0.330 Chirality : 0.039 0.158 4920 Planarity : 0.004 0.047 6192 Dihedral : 4.465 20.165 4536 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.40 % Favored : 96.95 % 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: 4.32 (0.13), residues: 4032 helix: 3.20 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.20 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 63 TYR 0.025 0.003 TYR e 39 PHE 0.016 0.004 PHE W 81 TRP 0.013 0.003 TRP W 93 HIS 0.004 0.001 HIS O 57 Details of bonding type rmsd covalent geometry : bond 0.00293 (34776) covalent geometry : angle 0.60399 (46848) hydrogen bonds : bond 0.05808 ( 2712) hydrogen bonds : angle 3.87165 ( 8136) *********************** 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 653 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 629 time to evaluate : 1.542 Fit side-chains REVERT: 1 135 THR cc_start: 0.8561 (m) cc_final: 0.8317 (p) REVERT: 2 135 THR cc_start: 0.8558 (m) cc_final: 0.8322 (p) REVERT: 4 135 THR cc_start: 0.8571 (m) cc_final: 0.8338 (p) REVERT: A 135 THR cc_start: 0.8562 (m) cc_final: 0.8328 (p) REVERT: B 135 THR cc_start: 0.8561 (m) cc_final: 0.8329 (p) REVERT: E 135 THR cc_start: 0.8556 (m) cc_final: 0.8319 (p) REVERT: F 135 THR cc_start: 0.8567 (m) cc_final: 0.8333 (p) REVERT: H 135 THR cc_start: 0.8555 (m) cc_final: 0.8317 (p) REVERT: K 135 THR cc_start: 0.8567 (m) cc_final: 0.8333 (p) REVERT: O 135 THR cc_start: 0.8563 (m) cc_final: 0.8325 (p) REVERT: P 135 THR cc_start: 0.8557 (m) cc_final: 0.8321 (p) REVERT: S 135 THR cc_start: 0.8562 (m) cc_final: 0.8328 (p) REVERT: U 135 THR cc_start: 0.8568 (m) cc_final: 0.8338 (p) REVERT: X 135 THR cc_start: 0.8568 (m) cc_final: 0.8332 (p) REVERT: Y 135 THR cc_start: 0.8561 (m) cc_final: 0.8326 (p) REVERT: e 135 THR cc_start: 0.8574 (m) cc_final: 0.8342 (p) REVERT: r 135 THR cc_start: 0.8574 (m) cc_final: 0.8338 (p) outliers start: 24 outliers final: 24 residues processed: 644 average time/residue: 0.9160 time to fit residues: 678.6260 Evaluate side-chains 600 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 576 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 51 optimal weight: 30.0000 chunk 181 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 312 optimal weight: 0.9990 chunk 327 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 282 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 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 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.151101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.139455 restraints weight = 200460.322| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.76 r_work: 0.2796 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34776 Z= 0.197 Angle : 0.675 6.052 46848 Z= 0.371 Chirality : 0.041 0.163 4920 Planarity : 0.005 0.069 6192 Dihedral : 4.567 22.371 4536 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 3.30 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.93 (0.13), residues: 4032 helix: 2.92 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.14 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 1 63 TYR 0.033 0.003 TYR G 39 PHE 0.024 0.005 PHE K 81 TRP 0.012 0.003 TRP X 93 HIS 0.006 0.002 HIS 6 57 Details of bonding type rmsd covalent geometry : bond 0.00402 (34776) covalent geometry : angle 0.67538 (46848) hydrogen bonds : bond 0.06489 ( 2712) hydrogen bonds : angle 4.05467 ( 8136) *********************** 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 619 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 595 time to evaluate : 1.430 Fit side-chains REVERT: 1 135 THR cc_start: 0.8599 (m) cc_final: 0.8352 (p) REVERT: 2 135 THR cc_start: 0.8601 (m) cc_final: 0.8354 (p) REVERT: 4 135 THR cc_start: 0.8615 (m) cc_final: 0.8370 (p) REVERT: A 135 THR cc_start: 0.8609 (m) cc_final: 0.8365 (p) REVERT: B 135 THR cc_start: 0.8604 (m) cc_final: 0.8358 (p) REVERT: E 135 THR cc_start: 0.8610 (m) cc_final: 0.8364 (p) REVERT: F 135 THR cc_start: 0.8593 (m) cc_final: 0.8347 (p) REVERT: H 135 THR cc_start: 0.8598 (m) cc_final: 0.8351 (p) REVERT: K 135 THR cc_start: 0.8609 (m) cc_final: 0.8364 (p) REVERT: O 135 THR cc_start: 0.8614 (m) cc_final: 0.8368 (p) REVERT: P 135 THR cc_start: 0.8609 (m) cc_final: 0.8365 (p) REVERT: S 135 THR cc_start: 0.8602 (m) cc_final: 0.8357 (p) REVERT: U 135 THR cc_start: 0.8590 (m) cc_final: 0.8351 (p) REVERT: X 135 THR cc_start: 0.8608 (m) cc_final: 0.8363 (p) REVERT: Y 135 THR cc_start: 0.8606 (m) cc_final: 0.8364 (p) REVERT: e 135 THR cc_start: 0.8590 (m) cc_final: 0.8349 (p) REVERT: r 135 THR cc_start: 0.8596 (m) cc_final: 0.8351 (p) outliers start: 24 outliers final: 24 residues processed: 616 average time/residue: 0.8995 time to fit residues: 639.4234 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 : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 368 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 363 optimal weight: 2.9990 chunk 401 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 2 136 HIS 4 14 GLN 4 136 HIS 6 14 GLN A 14 GLN A 136 HIS B 14 GLN E 14 GLN E 136 HIS F 14 GLN F 136 HIS G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN O 136 HIS P 14 GLN Q 14 GLN S 14 GLN S 136 HIS U 14 GLN U 136 HIS W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN e 136 HIS r 14 GLN r 75 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.154768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.142927 restraints weight = 200501.186| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.76 r_work: 0.2850 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 34776 Z= 0.124 Angle : 0.538 5.413 46848 Z= 0.295 Chirality : 0.037 0.151 4920 Planarity : 0.004 0.063 6192 Dihedral : 4.390 22.298 4536 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 4.17 % Favored : 95.18 % 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: 4.63 (0.13), residues: 4032 helix: 3.44 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.20 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 1 63 TYR 0.021 0.002 TYR I 39 PHE 0.011 0.003 PHE A 41 TRP 0.012 0.002 TRP I 93 HIS 0.003 0.001 HIS W 128 Details of bonding type rmsd covalent geometry : bond 0.00227 (34776) covalent geometry : angle 0.53822 (46848) hydrogen bonds : bond 0.05244 ( 2712) hydrogen bonds : angle 3.70286 ( 8136) *********************** 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 : 1.045 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 588 average time/residue: 0.8748 time to fit residues: 595.1824 Evaluate side-chains 611 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 587 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 0 optimal weight: 30.0000 chunk 313 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 170 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 373 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 360 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN B 136 HIS E 14 GLN F 14 GLN G 14 GLN H 14 GLN H 136 HIS I 14 GLN I 136 HIS K 14 GLN K 136 HIS M 14 GLN O 14 GLN P 14 GLN P 136 HIS Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN Y 136 HIS a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.153652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.142125 restraints weight = 199394.391| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.72 r_work: 0.2840 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1265 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= 0.133 Angle : 0.557 5.463 46848 Z= 0.305 Chirality : 0.037 0.150 4920 Planarity : 0.004 0.051 6192 Dihedral : 4.384 22.403 4536 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 4.25 % Favored : 95.10 % 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: 3.44 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.22 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 63 TYR 0.022 0.002 TYR B 39 PHE 0.014 0.003 PHE M 81 TRP 0.011 0.002 TRP W 93 HIS 0.003 0.001 HIS O 57 Details of bonding type rmsd covalent geometry : bond 0.00251 (34776) covalent geometry : angle 0.55665 (46848) hydrogen bonds : bond 0.05475 ( 2712) hydrogen bonds : angle 3.73436 ( 8136) *********************** 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 642 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 618 time to evaluate : 1.661 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 636 average time/residue: 0.9571 time to fit residues: 702.6312 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 : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 113 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 chunk 229 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.156429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.145016 restraints weight = 201912.435| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.75 r_work: 0.2874 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 34776 Z= 0.113 Angle : 0.505 5.190 46848 Z= 0.277 Chirality : 0.036 0.145 4920 Planarity : 0.003 0.057 6192 Dihedral : 4.277 22.078 4536 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.65 % Allowed : 4.30 % Favored : 95.04 % 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: 4.99 (0.13), residues: 4032 helix: 3.70 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.23 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 1 63 TYR 0.019 0.002 TYR 1 39 PHE 0.010 0.002 PHE 1 132 TRP 0.011 0.002 TRP M 93 HIS 0.003 0.001 HIS K 128 Details of bonding type rmsd covalent geometry : bond 0.00201 (34776) covalent geometry : angle 0.50533 (46848) hydrogen bonds : bond 0.04839 ( 2712) hydrogen bonds : angle 3.56442 ( 8136) *********************** 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 611 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 587 time to evaluate : 1.455 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 606 average time/residue: 0.8986 time to fit residues: 625.8940 Evaluate side-chains 592 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 574 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS 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: 5.9990 chunk 361 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 170 optimal weight: 30.0000 chunk 276 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 300 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.152323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.140620 restraints weight = 196976.212| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.75 r_work: 0.2814 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34776 Z= 0.173 Angle : 0.630 5.774 46848 Z= 0.346 Chirality : 0.040 0.153 4920 Planarity : 0.005 0.058 6192 Dihedral : 4.443 22.393 4536 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.14 % Allowed : 3.84 % Favored : 95.02 % 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: 4.41 (0.13), residues: 4032 helix: 3.26 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.28 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 63 TYR 0.029 0.003 TYR r 39 PHE 0.022 0.004 PHE G 81 TRP 0.010 0.003 TRP P 93 HIS 0.005 0.002 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00346 (34776) covalent geometry : angle 0.63028 (46848) hydrogen bonds : bond 0.06078 ( 2712) hydrogen bonds : angle 3.91132 ( 8136) *********************** 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 638 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 596 time to evaluate : 1.475 Fit side-chains outliers start: 42 outliers final: 32 residues processed: 614 average time/residue: 0.8509 time to fit residues: 605.0123 Evaluate side-chains 580 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 548 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 94 GLU Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 94 GLU Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 147 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 305 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.154742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.143260 restraints weight = 201434.050| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.74 r_work: 0.2849 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1317 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= 0.126 Angle : 0.547 5.362 46848 Z= 0.300 Chirality : 0.037 0.150 4920 Planarity : 0.004 0.051 6192 Dihedral : 4.338 22.316 4536 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.03 % Allowed : 3.95 % Favored : 95.02 % 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: 4.73 (0.13), residues: 4032 helix: 3.50 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.24 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 63 TYR 0.021 0.002 TYR 2 39 PHE 0.012 0.003 PHE I 81 TRP 0.012 0.002 TRP I 93 HIS 0.003 0.001 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00234 (34776) covalent geometry : angle 0.54697 (46848) hydrogen bonds : bond 0.05249 ( 2712) hydrogen bonds : angle 3.68711 ( 8136) ********************** 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 602 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 564 time to evaluate : 1.377 Fit side-chains outliers start: 38 outliers final: 32 residues processed: 588 average time/residue: 0.9039 time to fit residues: 612.9231 Evaluate side-chains 595 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 563 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 94 GLU Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 94 GLU Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 313 optimal weight: 0.9990 chunk 336 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 347 optimal weight: 1.9990 chunk 387 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.153716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.142113 restraints weight = 199060.383| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.76 r_work: 0.2832 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34776 Z= 0.140 Angle : 0.577 5.815 46848 Z= 0.317 Chirality : 0.038 0.148 4920 Planarity : 0.004 0.044 6192 Dihedral : 4.381 22.384 4536 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.31 % Allowed : 3.68 % Favored : 95.02 % 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: 4.60 (0.13), residues: 4032 helix: 3.41 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.24 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 63 TYR 0.024 0.002 TYR r 39 PHE 0.015 0.003 PHE B 81 TRP 0.012 0.003 TRP O 93 HIS 0.004 0.001 HIS 2 57 Details of bonding type rmsd covalent geometry : bond 0.00268 (34776) covalent geometry : angle 0.57711 (46848) hydrogen bonds : bond 0.05573 ( 2712) hydrogen bonds : angle 3.76906 ( 8136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18431.06 seconds wall clock time: 313 minutes 31.96 seconds (18811.96 seconds total)