Starting phenix.real_space_refine on Sun Jun 29 09:14:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpx_16789/06_2025/8cpx_16789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpx_16789/06_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_16789/06_2025/8cpx_16789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpx_16789/06_2025/8cpx_16789.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpx_16789/06_2025/8cpx_16789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpx_16789/06_2025/8cpx_16789.cif" } resolution = 1.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.69, per 1000 atoms: 0.58 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: 9.77 Conformation dependent library (CDL) restraints added in 4.1 seconds 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: 3.24 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: 11.85 Time building geometry restraints manager: 11.32 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 176 or resid 201)) selection = (chain '2' and (resid 4 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 176 or resid 500)) selection = (chain 'B' and (resid 4 through 176 or resid 500)) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid 4 through 176 or resid 201)) selection = (chain 'H' and (resid 4 through 176 or resid 201)) selection = chain 'I' selection = chain 'K' selection = (chain 'M' and (resid 4 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 176 or resid 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.250 Set scattering table: 0.280 Process input model: 76.410 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.240 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.004 TRP H 93 HIS 0.011 0.004 HIS 1 151 PHE 0.028 0.005 PHE G 41 TYR 0.117 0.008 TYR F 32 ARG 0.021 0.004 ARG P 63 Details of bonding type rmsd hydrogen bonds : bond 0.07434 ( 2712) hydrogen bonds : angle 4.49585 ( 8136) covalent geometry : bond 0.00492 (34776) covalent geometry : angle 0.80295 (46848) *********************** 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 : 4.321 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: 1.8812 time to fit residues: 1601.2078 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 : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 0.5980 chunk 165 optimal weight: 9.9990 chunk 319 optimal weight: 0.1980 chunk 123 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 370 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 75 GLN r 112 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.154484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.142962 restraints weight = 202538.086| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.78 r_work: 0.2855 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0959 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= 0.128 Angle : 0.554 5.692 46848 Z= 0.307 Chirality : 0.038 0.158 4920 Planarity : 0.004 0.052 6192 Dihedral : 4.487 20.523 4536 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.18 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.13), residues: 4032 helix: 3.33 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.13 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 93 HIS 0.005 0.001 HIS Y 128 PHE 0.017 0.003 PHE a 41 TYR 0.043 0.003 TYR B 32 ARG 0.005 0.000 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.05256 ( 2712) hydrogen bonds : angle 3.72559 ( 8136) covalent geometry : bond 0.00234 (34776) covalent geometry : angle 0.55414 (46848) *********************** 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 597 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 573 time to evaluate : 4.022 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 595 average time/residue: 2.4637 time to fit residues: 1695.9595 Evaluate side-chains 563 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 539 time to evaluate : 3.925 ------------------------------------------------------------------------------- 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 205 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 308 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 0.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 0.2980 overall best weight: 3.2386 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.151372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.139956 restraints weight = 202631.142| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.77 r_work: 0.2802 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34776 Z= 0.169 Angle : 0.643 6.166 46848 Z= 0.354 Chirality : 0.040 0.160 4920 Planarity : 0.004 0.056 6192 Dihedral : 4.501 19.891 4536 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.71 % Allowed : 2.94 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.13), residues: 4032 helix: 3.19 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.13 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP X 93 HIS 0.005 0.002 HIS a 57 PHE 0.018 0.004 PHE a 41 TYR 0.036 0.004 TYR A 32 ARG 0.008 0.001 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.06129 ( 2712) hydrogen bonds : angle 3.94630 ( 8136) covalent geometry : bond 0.00339 (34776) covalent geometry : angle 0.64331 (46848) *********************** 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 607 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 581 time to evaluate : 4.503 Fit side-chains REVERT: 1 135 THR cc_start: 0.8612 (m) cc_final: 0.8327 (p) REVERT: 2 135 THR cc_start: 0.8607 (m) cc_final: 0.8321 (p) REVERT: 4 135 THR cc_start: 0.8609 (m) cc_final: 0.8323 (p) REVERT: A 135 THR cc_start: 0.8606 (m) cc_final: 0.8318 (p) REVERT: B 135 THR cc_start: 0.8605 (m) cc_final: 0.8322 (p) REVERT: E 135 THR cc_start: 0.8614 (m) cc_final: 0.8326 (p) REVERT: F 135 THR cc_start: 0.8603 (m) cc_final: 0.8339 (p) REVERT: H 135 THR cc_start: 0.8604 (m) cc_final: 0.8318 (p) REVERT: K 135 THR cc_start: 0.8614 (m) cc_final: 0.8328 (p) REVERT: O 135 THR cc_start: 0.8617 (m) cc_final: 0.8331 (p) REVERT: P 135 THR cc_start: 0.8605 (m) cc_final: 0.8342 (p) REVERT: S 135 THR cc_start: 0.8602 (m) cc_final: 0.8315 (p) REVERT: U 135 THR cc_start: 0.8598 (m) cc_final: 0.8334 (p) REVERT: X 135 THR cc_start: 0.8610 (m) cc_final: 0.8324 (p) REVERT: Y 135 THR cc_start: 0.8609 (m) cc_final: 0.8323 (p) REVERT: e 135 THR cc_start: 0.8607 (m) cc_final: 0.8320 (p) REVERT: r 135 THR cc_start: 0.8614 (m) cc_final: 0.8327 (p) outliers start: 26 outliers final: 24 residues processed: 603 average time/residue: 2.6243 time to fit residues: 1837.0759 Evaluate side-chains 591 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 567 time to evaluate : 3.628 ------------------------------------------------------------------------------- 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 366 optimal weight: 10.0000 chunk 279 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 7.9990 chunk 194 optimal weight: 0.6980 chunk 353 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.152741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.141522 restraints weight = 200384.976| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.78 r_work: 0.2824 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1136 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= 0.141 Angle : 0.574 5.577 46848 Z= 0.316 Chirality : 0.038 0.155 4920 Planarity : 0.004 0.045 6192 Dihedral : 4.451 22.175 4536 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 3.54 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.50 (0.13), residues: 4032 helix: 3.34 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.20 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP O 93 HIS 0.003 0.001 HIS 6 57 PHE 0.015 0.003 PHE 1 41 TYR 0.023 0.003 TYR I 39 ARG 0.005 0.000 ARG a 63 Details of bonding type rmsd hydrogen bonds : bond 0.05621 ( 2712) hydrogen bonds : angle 3.79768 ( 8136) covalent geometry : bond 0.00271 (34776) covalent geometry : angle 0.57387 (46848) *********************** 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 646 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 622 time to evaluate : 4.480 Fit side-chains REVERT: 1 135 THR cc_start: 0.8561 (m) cc_final: 0.8319 (p) REVERT: 2 135 THR cc_start: 0.8545 (m) cc_final: 0.8312 (p) REVERT: 4 135 THR cc_start: 0.8548 (m) cc_final: 0.8316 (p) REVERT: A 135 THR cc_start: 0.8550 (m) cc_final: 0.8319 (p) REVERT: B 135 THR cc_start: 0.8537 (m) cc_final: 0.8306 (p) REVERT: E 135 THR cc_start: 0.8549 (m) cc_final: 0.8315 (p) REVERT: F 135 THR cc_start: 0.8553 (m) cc_final: 0.8324 (p) REVERT: H 135 THR cc_start: 0.8547 (m) cc_final: 0.8313 (p) REVERT: K 135 THR cc_start: 0.8556 (m) cc_final: 0.8326 (p) REVERT: O 135 THR cc_start: 0.8549 (m) cc_final: 0.8314 (p) REVERT: P 135 THR cc_start: 0.8539 (m) cc_final: 0.8308 (p) REVERT: S 135 THR cc_start: 0.8542 (m) cc_final: 0.8312 (p) REVERT: U 135 THR cc_start: 0.8534 (m) cc_final: 0.8304 (p) REVERT: X 135 THR cc_start: 0.8551 (m) cc_final: 0.8317 (p) REVERT: Y 135 THR cc_start: 0.8551 (m) cc_final: 0.8321 (p) REVERT: e 135 THR cc_start: 0.8545 (m) cc_final: 0.8312 (p) REVERT: r 135 THR cc_start: 0.8549 (m) cc_final: 0.8315 (p) outliers start: 24 outliers final: 24 residues processed: 640 average time/residue: 1.9380 time to fit residues: 1435.6591 Evaluate side-chains 607 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 583 time to evaluate : 4.197 ------------------------------------------------------------------------------- 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 328 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.151267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.139620 restraints weight = 200439.494| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.76 r_work: 0.2798 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34776 Z= 0.191 Angle : 0.664 5.944 46848 Z= 0.365 Chirality : 0.041 0.162 4920 Planarity : 0.005 0.064 6192 Dihedral : 4.522 22.185 4536 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.71 % Allowed : 3.05 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.13), residues: 4032 helix: 3.04 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.15 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP W 93 HIS 0.006 0.002 HIS Y 57 PHE 0.023 0.005 PHE S 81 TYR 0.032 0.003 TYR e 39 ARG 0.008 0.001 ARG a 63 Details of bonding type rmsd hydrogen bonds : bond 0.06395 ( 2712) hydrogen bonds : angle 4.01860 ( 8136) covalent geometry : bond 0.00388 (34776) covalent geometry : angle 0.66387 (46848) *********************** 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 623 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 597 time to evaluate : 4.257 Fit side-chains REVERT: 1 135 THR cc_start: 0.8613 (m) cc_final: 0.8352 (p) REVERT: 2 135 THR cc_start: 0.8602 (m) cc_final: 0.8342 (p) REVERT: 4 135 THR cc_start: 0.8607 (m) cc_final: 0.8349 (p) REVERT: A 135 THR cc_start: 0.8606 (m) cc_final: 0.8350 (p) REVERT: B 135 THR cc_start: 0.8600 (m) cc_final: 0.8342 (p) REVERT: E 135 THR cc_start: 0.8609 (m) cc_final: 0.8349 (p) REVERT: F 135 THR cc_start: 0.8607 (m) cc_final: 0.8350 (p) REVERT: H 135 THR cc_start: 0.8605 (m) cc_final: 0.8345 (p) REVERT: K 135 THR cc_start: 0.8610 (m) cc_final: 0.8353 (p) REVERT: O 135 THR cc_start: 0.8615 (m) cc_final: 0.8357 (p) REVERT: P 135 THR cc_start: 0.8607 (m) cc_final: 0.8350 (p) REVERT: S 135 THR cc_start: 0.8598 (m) cc_final: 0.8339 (p) REVERT: U 135 THR cc_start: 0.8597 (m) cc_final: 0.8338 (p) REVERT: X 135 THR cc_start: 0.8610 (m) cc_final: 0.8352 (p) REVERT: Y 135 THR cc_start: 0.8603 (m) cc_final: 0.8344 (p) REVERT: e 135 THR cc_start: 0.8602 (m) cc_final: 0.8344 (p) REVERT: r 135 THR cc_start: 0.8611 (m) cc_final: 0.8353 (p) outliers start: 26 outliers final: 24 residues processed: 619 average time/residue: 1.9548 time to fit residues: 1403.7082 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 : 4.264 ------------------------------------------------------------------------------- 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 132 optimal weight: 9.9990 chunk 355 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 394 optimal weight: 8.9990 chunk 327 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 B 136 HIS E 14 GLN E 136 HIS F 14 GLN F 136 HIS 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 O 136 HIS P 14 GLN P 136 HIS Q 14 GLN S 14 GLN S 136 HIS U 14 GLN U 136 HIS W 14 GLN X 14 GLN Y 14 GLN Y 136 HIS a 14 GLN e 14 GLN e 136 HIS r 14 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.152895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.141110 restraints weight = 200321.724| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.76 r_work: 0.2822 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1186 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= 0.149 Angle : 0.592 5.602 46848 Z= 0.325 Chirality : 0.039 0.158 4920 Planarity : 0.004 0.046 6192 Dihedral : 4.459 22.137 4536 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 3.79 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.37 (0.13), residues: 4032 helix: 3.24 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.21 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP 6 93 HIS 0.004 0.001 HIS G 57 PHE 0.015 0.003 PHE M 81 TYR 0.024 0.003 TYR e 39 ARG 0.007 0.001 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.05778 ( 2712) hydrogen bonds : angle 3.84041 ( 8136) covalent geometry : bond 0.00290 (34776) covalent geometry : angle 0.59199 (46848) *********************** 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 621 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 597 time to evaluate : 5.528 Fit side-chains REVERT: 1 135 THR cc_start: 0.8558 (m) cc_final: 0.8335 (p) REVERT: 2 135 THR cc_start: 0.8566 (m) cc_final: 0.8338 (p) REVERT: 4 135 THR cc_start: 0.8572 (m) cc_final: 0.8347 (p) REVERT: A 135 THR cc_start: 0.8570 (m) cc_final: 0.8347 (p) REVERT: B 135 THR cc_start: 0.8560 (m) cc_final: 0.8335 (p) REVERT: E 135 THR cc_start: 0.8551 (m) cc_final: 0.8325 (p) REVERT: F 135 THR cc_start: 0.8558 (m) cc_final: 0.8337 (p) REVERT: H 135 THR cc_start: 0.8559 (m) cc_final: 0.8331 (p) REVERT: K 135 THR cc_start: 0.8572 (m) cc_final: 0.8348 (p) REVERT: O 135 THR cc_start: 0.8568 (m) cc_final: 0.8343 (p) REVERT: P 135 THR cc_start: 0.8555 (m) cc_final: 0.8332 (p) REVERT: S 135 THR cc_start: 0.8560 (m) cc_final: 0.8337 (p) REVERT: U 135 THR cc_start: 0.8552 (m) cc_final: 0.8333 (p) REVERT: X 135 THR cc_start: 0.8563 (m) cc_final: 0.8340 (p) REVERT: Y 135 THR cc_start: 0.8558 (m) cc_final: 0.8333 (p) REVERT: e 135 THR cc_start: 0.8566 (m) cc_final: 0.8339 (p) REVERT: r 135 THR cc_start: 0.8569 (m) cc_final: 0.8345 (p) outliers start: 24 outliers final: 24 residues processed: 621 average time/residue: 2.0304 time to fit residues: 1471.2079 Evaluate side-chains 630 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 606 time to evaluate : 5.766 ------------------------------------------------------------------------------- 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 380 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 224 optimal weight: 0.4980 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.153872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.142336 restraints weight = 199281.173| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.72 r_work: 0.2844 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1230 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= 0.129 Angle : 0.549 5.444 46848 Z= 0.301 Chirality : 0.037 0.151 4920 Planarity : 0.004 0.043 6192 Dihedral : 4.396 22.260 4536 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.65 % Allowed : 3.89 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.13), residues: 4032 helix: 3.45 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.23 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 93 HIS 0.003 0.001 HIS F 57 PHE 0.013 0.003 PHE r 81 TYR 0.021 0.002 TYR 1 39 ARG 0.008 0.000 ARG K 63 Details of bonding type rmsd hydrogen bonds : bond 0.05381 ( 2712) hydrogen bonds : angle 3.72405 ( 8136) covalent geometry : bond 0.00242 (34776) covalent geometry : angle 0.54905 (46848) *********************** 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 612 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 588 time to evaluate : 6.800 Fit side-chains REVERT: 1 135 THR cc_start: 0.8539 (m) cc_final: 0.8332 (p) REVERT: 2 135 THR cc_start: 0.8550 (m) cc_final: 0.8340 (p) REVERT: 4 135 THR cc_start: 0.8558 (m) cc_final: 0.8350 (p) REVERT: A 135 THR cc_start: 0.8551 (m) cc_final: 0.8345 (p) REVERT: E 135 THR cc_start: 0.8553 (m) cc_final: 0.8343 (p) REVERT: H 135 THR cc_start: 0.8551 (m) cc_final: 0.8340 (p) REVERT: O 135 THR cc_start: 0.8565 (m) cc_final: 0.8359 (p) REVERT: U 135 THR cc_start: 0.8546 (m) cc_final: 0.8340 (p) REVERT: e 135 THR cc_start: 0.8535 (m) cc_final: 0.8325 (p) outliers start: 24 outliers final: 24 residues processed: 607 average time/residue: 2.3371 time to fit residues: 1660.8263 Evaluate side-chains 571 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 547 time to evaluate : 3.888 ------------------------------------------------------------------------------- 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 243 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.154098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.142560 restraints weight = 200582.932| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.76 r_work: 0.2840 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 34776 Z= 0.131 Angle : 0.552 5.364 46848 Z= 0.303 Chirality : 0.037 0.148 4920 Planarity : 0.004 0.042 6192 Dihedral : 4.380 22.370 4536 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.31 % Allowed : 3.46 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.68 (0.13), residues: 4032 helix: 3.47 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.23 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 93 HIS 0.003 0.001 HIS P 57 PHE 0.014 0.003 PHE M 81 TYR 0.022 0.002 TYR 1 39 ARG 0.009 0.000 ARG r 63 Details of bonding type rmsd hydrogen bonds : bond 0.05406 ( 2712) hydrogen bonds : angle 3.71875 ( 8136) covalent geometry : bond 0.00245 (34776) covalent geometry : angle 0.55214 (46848) *********************** 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 606 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 558 time to evaluate : 4.378 Fit side-chains REVERT: 1 135 THR cc_start: 0.8551 (m) cc_final: 0.8343 (p) REVERT: E 135 THR cc_start: 0.8553 (m) cc_final: 0.8345 (p) REVERT: O 135 THR cc_start: 0.8563 (m) cc_final: 0.8360 (p) REVERT: U 135 THR cc_start: 0.8548 (m) cc_final: 0.8346 (p) outliers start: 48 outliers final: 48 residues processed: 581 average time/residue: 1.9884 time to fit residues: 1340.5964 Evaluate side-chains 616 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 568 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 94 GLU 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 94 GLU Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 94 GLU 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 G residue 119 LYS Chi-restraints excluded: chain H 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 M residue 119 LYS Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q 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 W residue 119 LYS 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 a residue 119 LYS Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 94 GLU 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 357 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 287 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 20.0000 chunk 346 optimal weight: 0.9980 chunk 365 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.154067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.142354 restraints weight = 197511.733| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.75 r_work: 0.2838 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1225 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= 0.134 Angle : 0.560 5.400 46848 Z= 0.307 Chirality : 0.037 0.148 4920 Planarity : 0.004 0.040 6192 Dihedral : 4.382 22.406 4536 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.31 % Allowed : 3.40 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.65 (0.13), residues: 4032 helix: 3.45 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.24 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 2 93 HIS 0.003 0.001 HIS P 57 PHE 0.014 0.003 PHE 4 81 TYR 0.023 0.002 TYR E 39 ARG 0.010 0.001 ARG r 63 Details of bonding type rmsd hydrogen bonds : bond 0.05465 ( 2712) hydrogen bonds : angle 3.73361 ( 8136) covalent geometry : bond 0.00254 (34776) covalent geometry : angle 0.56047 (46848) *********************** 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 640 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 592 time to evaluate : 4.749 Fit side-chains REVERT: 1 135 THR cc_start: 0.8548 (m) cc_final: 0.8338 (p) REVERT: E 135 THR cc_start: 0.8551 (m) cc_final: 0.8343 (p) REVERT: O 135 THR cc_start: 0.8565 (m) cc_final: 0.8362 (p) REVERT: U 135 THR cc_start: 0.8551 (m) cc_final: 0.8348 (p) outliers start: 48 outliers final: 48 residues processed: 615 average time/residue: 1.9513 time to fit residues: 1394.6355 Evaluate side-chains 614 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 566 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 94 GLU 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 94 GLU Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 94 GLU 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 G residue 119 LYS Chi-restraints excluded: chain H 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 M residue 119 LYS Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q 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 W residue 119 LYS 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 a residue 119 LYS Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 94 GLU 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 240 optimal weight: 0.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 406 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 0.2980 chunk 33 optimal weight: 20.0000 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.155619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.144039 restraints weight = 201073.757| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.75 r_work: 0.2862 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34776 Z= 0.118 Angle : 0.526 5.304 46848 Z= 0.288 Chirality : 0.036 0.146 4920 Planarity : 0.004 0.046 6192 Dihedral : 4.314 22.153 4536 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.31 % Allowed : 3.38 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.87 (0.13), residues: 4032 helix: 3.61 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.23 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 93 HIS 0.003 0.001 HIS A 128 PHE 0.011 0.003 PHE Q 41 TYR 0.020 0.002 TYR B 39 ARG 0.010 0.000 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 2712) hydrogen bonds : angle 3.61692 ( 8136) covalent geometry : bond 0.00215 (34776) covalent geometry : angle 0.52563 (46848) ********************** 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 626 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 578 time to evaluate : 4.263 Fit side-chains outliers start: 48 outliers final: 42 residues processed: 602 average time/residue: 1.8795 time to fit residues: 1312.8406 Evaluate side-chains 613 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 571 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 94 GLU 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 94 GLU Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 94 GLU 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 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 94 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 94 GLU 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 94 GLU Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 94 GLU 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 257 optimal weight: 0.9990 chunk 344 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 332 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 G 60 HIS 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.152217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.140655 restraints weight = 198160.708| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.77 r_work: 0.2810 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1164 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= 0.178 Angle : 0.639 5.781 46848 Z= 0.351 Chirality : 0.040 0.159 4920 Planarity : 0.004 0.060 6192 Dihedral : 4.458 22.457 4536 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.14 % Allowed : 3.70 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.35 (0.13), residues: 4032 helix: 3.21 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.25 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP 4 93 HIS 0.006 0.002 HIS E 60 PHE 0.023 0.004 PHE K 81 TYR 0.031 0.003 TYR A 39 ARG 0.013 0.001 ARG r 63 Details of bonding type rmsd hydrogen bonds : bond 0.06142 ( 2712) hydrogen bonds : angle 3.93463 ( 8136) covalent geometry : bond 0.00358 (34776) covalent geometry : angle 0.63909 (46848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41841.13 seconds wall clock time: 730 minutes 22.62 seconds (43822.62 seconds total)