Starting phenix.real_space_refine on Sun Jun 29 11:45:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpw_16788/06_2025/8cpw_16788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpw_16788/06_2025/8cpw_16788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cpw_16788/06_2025/8cpw_16788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpw_16788/06_2025/8cpw_16788.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpw_16788/06_2025/8cpw_16788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpw_16788/06_2025/8cpw_16788.cif" } resolution = 1.79 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 8510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 36004 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "2" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "4" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "6" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "H" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "O" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Q" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "S" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "U" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "W" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "X" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "Y" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "a" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "e" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "r" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Time building chain proxies: 21.75, per 1000 atoms: 0.60 Number of scatterers: 36004 At special positions: 0 Unit cell: (131.856, 131.856, 131.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 Mg 14 11.99 Na 24 11.00 O 8510 8.00 N 5976 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.78 Conformation dependent library (CDL) restraints added in 4.0 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 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 77 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 163 through 174 Processing helix chain '2' and resid 13 through 42 Processing helix chain '2' and resid 48 through 77 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 163 through 174 Processing helix chain '4' and resid 13 through 42 Processing helix chain '4' and resid 48 through 77 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 163 through 174 Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 48 through 76 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 163 through 174 Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 77 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 Processing helix chain 'a' and resid 13 through 42 Processing helix chain 'a' and resid 48 through 76 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 163 through 174 Processing helix chain 'e' and resid 13 through 42 Processing helix chain 'e' and resid 48 through 77 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 163 through 174 Processing helix chain 'r' and resid 13 through 42 Processing helix chain 'r' and resid 48 through 77 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 163 through 174 2706 hydrogen bonds defined for protein. 8118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.83 Time building geometry restraints manager: 10.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11624 1.34 - 1.46: 4988 1.46 - 1.57: 17900 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.755 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" CB CSX G 90 " pdb=" SG CSX G 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX Q 90 " pdb=" SG CSX Q 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CB CSX K 90 " pdb=" SG CSX K 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 42306 1.33 - 2.66: 3801 2.66 - 3.99: 563 3.99 - 5.32: 130 5.32 - 6.65: 48 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR E 39 " pdb=" CB TYR E 39 " pdb=" CG TYR E 39 " ideal model delta sigma weight residual 113.90 108.14 5.76 1.80e+00 3.09e-01 1.02e+01 angle pdb=" CA TYR I 39 " pdb=" CB TYR I 39 " pdb=" CG TYR I 39 " ideal model delta sigma weight residual 113.90 108.16 5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" CA TYR 2 39 " pdb=" CB TYR 2 39 " pdb=" CG TYR 2 39 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR 4 39 " pdb=" CB TYR 4 39 " pdb=" CG TYR 4 39 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR M 39 " pdb=" CB TYR M 39 " pdb=" CG TYR M 39 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 18967 16.52 - 33.04: 1481 33.04 - 49.55: 347 49.55 - 66.07: 96 66.07 - 82.59: 109 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL U 46 " pdb=" C VAL U 46 " pdb=" N ALA U 47 " pdb=" CA ALA U 47 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N ALA E 47 " pdb=" CA ALA E 47 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3454 0.056 - 0.112: 1163 0.112 - 0.168: 212 0.168 - 0.225: 68 0.225 - 0.281: 23 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR I 137 " pdb=" N TYR I 137 " pdb=" C TYR I 137 " pdb=" CB TYR I 137 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA TYR O 137 " pdb=" N TYR O 137 " pdb=" C TYR O 137 " pdb=" CB TYR O 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR E 137 " pdb=" N TYR E 137 " pdb=" C TYR E 137 " pdb=" CB TYR E 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 137 " -0.023 2.00e-02 2.50e+03 1.69e-02 5.69e+00 pdb=" CG TYR 2 137 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 137 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 137 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 137 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 2 137 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR 2 137 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 137 " 0.023 2.00e-02 2.50e+03 1.68e-02 5.66e+00 pdb=" CG TYR 1 137 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 137 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 137 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 137 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR 1 137 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR 1 137 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 137 " 0.023 2.00e-02 2.50e+03 1.68e-02 5.65e+00 pdb=" CG TYR A 137 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 137 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 137 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 137 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 137 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 137 " 0.021 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2972 2.72 - 3.27: 39534 3.27 - 3.81: 71869 3.81 - 4.36: 89786 4.36 - 4.90: 141783 Nonbonded interactions: 345944 Sorted by model distance: nonbonded pdb=" OE1 GLU M 116 " pdb=" O HOH M 301 " model vdw 2.180 3.040 nonbonded pdb=" OE1 GLU Q 116 " pdb=" O HOH Q 601 " model vdw 2.181 3.040 nonbonded pdb=" OE1 GLU W 116 " pdb=" O HOH W 601 " model vdw 2.181 3.040 nonbonded pdb=" OE1 GLU a 116 " pdb=" O HOH a 301 " model vdw 2.181 3.040 nonbonded pdb=" OE1 GLU 6 116 " pdb=" O HOH 6 301 " model vdw 2.181 3.040 ... (remaining 345939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain '1' and resid 4 through 176) selection = (chain '2' and resid 4 through 176) selection = (chain '4' and resid 4 through 176) selection = (chain '6' and resid 4 through 176) selection = (chain 'A' and resid 4 through 176) selection = (chain 'B' and resid 4 through 176) selection = (chain 'E' and resid 4 through 176) selection = (chain 'F' and resid 4 through 176) selection = (chain 'G' and resid 4 through 176) selection = (chain 'H' and resid 4 through 176) selection = (chain 'I' and resid 4 through 176) selection = (chain 'K' and resid 4 through 176) selection = (chain 'M' and resid 4 through 176) selection = (chain 'O' and resid 4 through 176) selection = (chain 'P' and resid 4 through 176) selection = (chain 'Q' and resid 4 through 176) selection = (chain 'S' and resid 4 through 176) selection = (chain 'U' and resid 4 through 176) selection = (chain 'W' and resid 4 through 176) selection = (chain 'X' and resid 4 through 176) selection = (chain 'Y' and resid 4 through 176) selection = (chain 'a' and resid 4 through 176) selection = (chain 'e' and resid 4 through 176) selection = (chain 'r' and resid 4 through 176) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 1.540 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 76.460 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.340 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:15.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 34776 Z= 0.256 Angle : 0.840 6.653 46848 Z= 0.483 Chirality : 0.060 0.281 4920 Planarity : 0.008 0.059 6192 Dihedral : 14.346 82.591 13032 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.63 % Allowed : 2.18 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.13), residues: 4032 helix: 1.61 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.83 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP e 93 HIS 0.011 0.004 HIS U 136 PHE 0.028 0.006 PHE K 41 TYR 0.029 0.006 TYR 1 137 ARG 0.015 0.003 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.08770 ( 2706) hydrogen bonds : angle 4.50203 ( 8118) covalent geometry : bond 0.00522 (34776) covalent geometry : angle 0.84008 (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 583 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 560 time to evaluate : 3.953 Fit side-chains REVERT: 2 70 MET cc_start: 0.8657 (mtp) cc_final: 0.8362 (mtp) REVERT: S 70 MET cc_start: 0.8657 (mtp) cc_final: 0.8360 (mtp) REVERT: W 70 MET cc_start: 0.8664 (mtp) cc_final: 0.8317 (mtp) REVERT: a 70 MET cc_start: 0.8668 (mtp) cc_final: 0.8323 (mtp) outliers start: 23 outliers final: 23 residues processed: 560 average time/residue: 2.0303 time to fit residues: 1315.0971 Evaluate side-chains 569 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 546 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 238 optimal weight: 0.0170 chunk 370 optimal weight: 5.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 14 GLN 2 112 GLN 4 112 GLN 6 14 GLN 6 112 GLN 6 125 ASN A 112 GLN B 14 GLN B 112 GLN B 125 ASN E 14 GLN E 112 GLN E 125 ASN F 14 GLN F 112 GLN G 112 GLN G 125 ASN H 14 GLN H 112 GLN I 112 GLN K 14 GLN K 112 GLN K 125 ASN M 14 GLN M 112 GLN O 112 GLN P 112 GLN Q 14 GLN Q 112 GLN S 14 GLN S 112 GLN U 14 GLN U 112 GLN U 125 ASN W 14 GLN W 112 GLN X 14 GLN X 112 GLN Y 14 GLN Y 112 GLN a 14 GLN a 112 GLN a 125 ASN e 112 GLN e 125 ASN r 112 GLN r 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.153240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.141387 restraints weight = 200144.109| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.77 r_work: 0.2760 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34776 Z= 0.171 Angle : 0.647 6.154 46848 Z= 0.361 Chirality : 0.042 0.158 4920 Planarity : 0.004 0.032 6192 Dihedral : 5.949 42.243 4582 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.12 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.08 (0.13), residues: 4032 helix: 3.08 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.94 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP I 93 HIS 0.006 0.002 HIS H 136 PHE 0.021 0.003 PHE X 41 TYR 0.023 0.003 TYR 2 39 ARG 0.008 0.001 ARG 6 63 Details of bonding type rmsd hydrogen bonds : bond 0.06082 ( 2706) hydrogen bonds : angle 3.95561 ( 8118) covalent geometry : bond 0.00341 (34776) covalent geometry : angle 0.64730 (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 624 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 600 time to evaluate : 4.218 Fit side-chains REVERT: 4 63 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7944 (tpt-90) REVERT: O 63 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7937 (tpt-90) REVERT: Q 63 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7951 (tpt-90) outliers start: 24 outliers final: 24 residues processed: 600 average time/residue: 1.9476 time to fit residues: 1354.6770 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 : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 1.9990 chunk 330 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 112 GLN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 112 GLN G 125 ASN H 125 ASN I 125 ASN K 112 GLN K 125 ASN M 112 GLN M 125 ASN O 125 ASN P 125 ASN Q 112 GLN Q 125 ASN S 125 ASN U 125 ASN W 112 GLN W 125 ASN X 125 ASN Y 125 ASN a 112 GLN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.151503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.139830 restraints weight = 202550.057| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.77 r_work: 0.2741 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 34776 Z= 0.263 Angle : 0.792 7.016 46848 Z= 0.440 Chirality : 0.046 0.156 4920 Planarity : 0.006 0.074 6192 Dihedral : 6.076 43.889 4582 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.96 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.63 (0.13), residues: 4032 helix: 2.75 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.85 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.004 TRP Y 93 HIS 0.011 0.003 HIS 4 60 PHE 0.029 0.005 PHE M 41 TYR 0.029 0.004 TYR M 39 ARG 0.009 0.002 ARG U 63 Details of bonding type rmsd hydrogen bonds : bond 0.07142 ( 2706) hydrogen bonds : angle 4.18467 ( 8118) covalent geometry : bond 0.00543 (34776) covalent geometry : angle 0.79156 (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 625 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 601 time to evaluate : 3.849 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 601 average time/residue: 1.9171 time to fit residues: 1332.6080 Evaluate side-chains 614 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 590 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 0.5980 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.155533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.144144 restraints weight = 202365.608| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.77 r_work: 0.2803 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 34776 Z= 0.129 Angle : 0.558 6.000 46848 Z= 0.309 Chirality : 0.038 0.144 4920 Planarity : 0.003 0.044 6192 Dihedral : 5.533 42.920 4582 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.02 % Favored : 97.33 % 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: 4.53 (0.13), residues: 4032 helix: 3.44 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.86 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 93 HIS 0.003 0.001 HIS M 105 PHE 0.016 0.002 PHE W 41 TYR 0.020 0.002 TYR H 39 ARG 0.008 0.001 ARG 4 63 Details of bonding type rmsd hydrogen bonds : bond 0.05338 ( 2706) hydrogen bonds : angle 3.69610 ( 8118) covalent geometry : bond 0.00239 (34776) covalent geometry : angle 0.55829 (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 584 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 560 time to evaluate : 4.593 Fit side-chains revert: symmetry clash REVERT: X 63 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7953 (tpt-90) outliers start: 24 outliers final: 24 residues processed: 560 average time/residue: 2.0239 time to fit residues: 1319.5105 Evaluate side-chains 582 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 558 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 293 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 336 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN M 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.152645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.141044 restraints weight = 202440.605| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.79 r_work: 0.2754 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34776 Z= 0.210 Angle : 0.706 7.040 46848 Z= 0.391 Chirality : 0.042 0.154 4920 Planarity : 0.005 0.087 6192 Dihedral : 5.702 43.686 4582 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.02 % Favored : 97.33 % 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: 4.15 (0.13), residues: 4032 helix: 3.15 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.86 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP M 93 HIS 0.009 0.002 HIS X 60 PHE 0.025 0.004 PHE A 41 TYR 0.027 0.003 TYR G 39 ARG 0.008 0.001 ARG O 63 Details of bonding type rmsd hydrogen bonds : bond 0.06600 ( 2706) hydrogen bonds : angle 4.00678 ( 8118) covalent geometry : bond 0.00428 (34776) covalent geometry : angle 0.70576 (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 603 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 579 time to evaluate : 4.664 Fit side-chains REVERT: 2 70 MET cc_start: 0.8867 (mtp) cc_final: 0.8646 (mtp) REVERT: S 70 MET cc_start: 0.8864 (mtp) cc_final: 0.8643 (mtp) outliers start: 24 outliers final: 24 residues processed: 579 average time/residue: 3.1500 time to fit residues: 2126.6426 Evaluate side-chains 588 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 564 time to evaluate : 8.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.154871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.143212 restraints weight = 200352.413| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.77 r_work: 0.2787 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 34776 Z= 0.142 Angle : 0.588 6.506 46848 Z= 0.325 Chirality : 0.039 0.143 4920 Planarity : 0.003 0.057 6192 Dihedral : 5.512 42.672 4582 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.02 % Favored : 97.33 % 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: 3.42 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.83 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP M 93 HIS 0.004 0.001 HIS E 136 PHE 0.018 0.003 PHE 2 41 TYR 0.023 0.002 TYR X 39 ARG 0.011 0.001 ARG 4 63 Details of bonding type rmsd hydrogen bonds : bond 0.05593 ( 2706) hydrogen bonds : angle 3.74338 ( 8118) covalent geometry : bond 0.00270 (34776) covalent geometry : angle 0.58848 (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 609 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 585 time to evaluate : 4.591 Fit side-chains revert: symmetry clash REVERT: 2 70 MET cc_start: 0.8886 (mtp) cc_final: 0.8601 (mtp) REVERT: S 70 MET cc_start: 0.8884 (mtp) cc_final: 0.8604 (mtp) outliers start: 24 outliers final: 24 residues processed: 585 average time/residue: 1.9079 time to fit residues: 1296.8209 Evaluate side-chains 582 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 558 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 7.9990 chunk 220 optimal weight: 20.0000 chunk 393 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.152249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.140613 restraints weight = 200366.209| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.74 r_work: 0.2754 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 34776 Z= 0.232 Angle : 0.746 7.332 46848 Z= 0.412 Chirality : 0.044 0.149 4920 Planarity : 0.005 0.092 6192 Dihedral : 5.722 43.762 4582 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.64 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.01 (0.13), residues: 4032 helix: 3.05 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.82 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP X 93 HIS 0.008 0.002 HIS O 136 PHE 0.027 0.004 PHE X 41 TYR 0.029 0.003 TYR O 39 ARG 0.017 0.002 ARG X 63 Details of bonding type rmsd hydrogen bonds : bond 0.06856 ( 2706) hydrogen bonds : angle 4.06652 ( 8118) covalent geometry : bond 0.00477 (34776) covalent geometry : angle 0.74575 (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 588 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 564 time to evaluate : 4.255 Fit side-chains revert: symmetry clash REVERT: 2 70 MET cc_start: 0.8874 (mtp) cc_final: 0.8620 (mtp) REVERT: S 70 MET cc_start: 0.8871 (mtp) cc_final: 0.8616 (mtp) outliers start: 24 outliers final: 24 residues processed: 564 average time/residue: 2.0045 time to fit residues: 1304.8301 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 : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 1 125 ASN 2 112 GLN 2 125 ASN 4 112 GLN 4 125 ASN 6 112 GLN 6 125 ASN A 112 GLN B 112 GLN B 125 ASN E 112 GLN F 112 GLN F 125 ASN G 112 GLN G 125 ASN H 112 GLN H 125 ASN I 112 GLN I 125 ASN K 112 GLN K 125 ASN M 112 GLN O 112 GLN O 125 ASN P 112 GLN P 125 ASN Q 112 GLN Q 125 ASN S 112 GLN S 125 ASN U 112 GLN W 112 GLN X 112 GLN Y 112 GLN Y 125 ASN a 112 GLN a 125 ASN e 112 GLN e 125 ASN r 112 GLN r 125 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.156040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.144574 restraints weight = 204359.272| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.76 r_work: 0.2810 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 34776 Z= 0.126 Angle : 0.558 6.244 46848 Z= 0.307 Chirality : 0.037 0.141 4920 Planarity : 0.003 0.053 6192 Dihedral : 5.409 41.908 4582 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.89 % Favored : 96.46 % 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: 3.54 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.82 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP a 93 HIS 0.003 0.001 HIS E 105 PHE 0.015 0.002 PHE r 41 TYR 0.021 0.002 TYR 2 39 ARG 0.011 0.001 ARG U 63 Details of bonding type rmsd hydrogen bonds : bond 0.05251 ( 2706) hydrogen bonds : angle 3.66030 ( 8118) covalent geometry : bond 0.00233 (34776) covalent geometry : angle 0.55765 (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 568 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 544 time to evaluate : 4.391 Fit side-chains revert: symmetry clash REVERT: G 70 MET cc_start: 0.8863 (mtp) cc_final: 0.8586 (mtp) outliers start: 24 outliers final: 1 residues processed: 544 average time/residue: 1.9478 time to fit residues: 1230.7162 Evaluate side-chains 538 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 537 time to evaluate : 4.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 1.9990 chunk 366 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 chunk 346 optimal weight: 0.9990 chunk 365 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.155411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.143809 restraints weight = 201168.996| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.74 r_work: 0.2797 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34776 Z= 0.139 Angle : 0.590 6.702 46848 Z= 0.325 Chirality : 0.038 0.139 4920 Planarity : 0.003 0.061 6192 Dihedral : 4.436 18.485 4536 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.86 % Favored : 96.49 % 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: 4.57 (0.13), residues: 4032 helix: 3.47 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.86 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP G 93 HIS 0.004 0.001 HIS B 105 PHE 0.017 0.003 PHE 4 41 TYR 0.023 0.002 TYR G 39 ARG 0.013 0.001 ARG O 63 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 2706) hydrogen bonds : angle 3.71243 ( 8118) covalent geometry : bond 0.00262 (34776) covalent geometry : angle 0.58960 (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 579 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 555 time to evaluate : 4.403 Fit side-chains REVERT: a 63 ARG cc_start: 0.8104 (ttp-170) cc_final: 0.7886 (tpt-90) outliers start: 24 outliers final: 24 residues processed: 555 average time/residue: 1.9584 time to fit residues: 1260.7139 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 : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 4.9990 chunk 374 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.152783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.141127 restraints weight = 201242.389| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.74 r_work: 0.2761 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34776 Z= 0.206 Angle : 0.710 7.443 46848 Z= 0.392 Chirality : 0.042 0.146 4920 Planarity : 0.004 0.084 6192 Dihedral : 4.573 16.803 4536 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.72 % Favored : 96.62 % 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: 4.21 (0.13), residues: 4032 helix: 3.20 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.82 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP W 93 HIS 0.007 0.002 HIS O 136 PHE 0.024 0.004 PHE K 41 TYR 0.029 0.003 TYR r 39 ARG 0.013 0.002 ARG O 63 Details of bonding type rmsd hydrogen bonds : bond 0.06548 ( 2706) hydrogen bonds : angle 3.96552 ( 8118) covalent geometry : bond 0.00419 (34776) covalent geometry : angle 0.70964 (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 576 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 552 time to evaluate : 4.153 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 552 average time/residue: 1.9830 time to fit residues: 1271.2682 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 : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 3.9990 chunk 344 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN B 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN P 125 ASN Q 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.158283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.146698 restraints weight = 199344.476| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.75 r_work: 0.2842 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 34776 Z= 0.115 Angle : 0.531 6.179 46848 Z= 0.292 Chirality : 0.037 0.140 4920 Planarity : 0.003 0.050 6192 Dihedral : 4.311 18.886 4536 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.91 % Favored : 96.43 % 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: 4.81 (0.13), residues: 4032 helix: 3.66 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.84 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 93 HIS 0.003 0.001 HIS 2 65 PHE 0.012 0.002 PHE O 41 TYR 0.019 0.002 TYR O 39 ARG 0.011 0.001 ARG U 63 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 2706) hydrogen bonds : angle 3.54493 ( 8118) covalent geometry : bond 0.00205 (34776) covalent geometry : angle 0.53082 (46848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38750.56 seconds wall clock time: 669 minutes 57.53 seconds (40197.53 seconds total)