Starting phenix.real_space_refine on Sun Jun 29 11:52:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpt_16785/06_2025/8cpt_16785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpt_16785/06_2025/8cpt_16785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cpt_16785/06_2025/8cpt_16785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpt_16785/06_2025/8cpt_16785.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpt_16785/06_2025/8cpt_16785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpt_16785/06_2025/8cpt_16785.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 8530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 36024 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "2" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "4" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "6" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "M" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "O" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Q" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "S" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "W" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "X" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Y" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "a" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "e" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "r" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Time building chain proxies: 22.28, per 1000 atoms: 0.62 Number of scatterers: 36024 At special positions: 0 Unit cell: (131.856, 131.856, 131.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 Mg 14 11.99 Na 24 11.00 O 8530 8.00 N 5976 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.86 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: 3.24 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 77 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 163 through 174 Processing helix chain '2' and resid 13 through 42 Processing helix chain '2' and resid 48 through 77 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 163 through 174 Processing helix chain '4' and resid 13 through 42 Processing helix chain '4' and resid 48 through 77 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 163 through 174 Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 48 through 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: 11.53 Time building geometry restraints manager: 11.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11640 1.34 - 1.46: 5268 1.46 - 1.57: 17604 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX X 90 " pdb=" SG CSX X 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CB CSX M 90 " pdb=" SG CSX M 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CB CSX B 90 " pdb=" SG CSX B 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CB CSX S 90 " pdb=" SG CSX S 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CB CSX F 90 " pdb=" SG CSX F 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 43085 1.17 - 2.35: 2975 2.35 - 3.52: 528 3.52 - 4.70: 177 4.70 - 5.87: 83 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR H 39 " pdb=" CB TYR H 39 " pdb=" CG TYR H 39 " ideal model delta sigma weight residual 113.90 108.03 5.87 1.80e+00 3.09e-01 1.06e+01 angle pdb=" CA TYR B 39 " pdb=" CB TYR B 39 " pdb=" CG TYR B 39 " ideal model delta sigma weight residual 113.90 108.10 5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA TYR A 39 " pdb=" CB TYR A 39 " pdb=" CG TYR A 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR 4 39 " pdb=" CB TYR 4 39 " pdb=" CG TYR 4 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR 1 39 " pdb=" CB TYR 1 39 " pdb=" CG TYR 1 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 19073 17.90 - 35.79: 1436 35.79 - 53.69: 276 53.69 - 71.58: 119 71.58 - 89.48: 96 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL A 46 " pdb=" C VAL A 46 " pdb=" N ALA A 47 " pdb=" CA ALA A 47 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N ALA E 47 " pdb=" CA ALA E 47 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL M 46 " pdb=" C VAL M 46 " pdb=" N ALA M 47 " pdb=" CA ALA M 47 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3523 0.047 - 0.094: 1050 0.094 - 0.141: 238 0.141 - 0.189: 67 0.189 - 0.236: 42 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR r 137 " pdb=" N TYR r 137 " pdb=" C TYR r 137 " pdb=" CB TYR r 137 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA TYR A 137 " pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CB TYR A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA TYR F 137 " pdb=" N TYR F 137 " pdb=" C TYR F 137 " pdb=" CB TYR F 137 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 137 " 0.025 2.00e-02 2.50e+03 1.82e-02 6.59e+00 pdb=" CG TYR P 137 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR P 137 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR P 137 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR P 137 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR P 137 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR P 137 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR P 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR r 137 " -0.025 2.00e-02 2.50e+03 1.81e-02 6.57e+00 pdb=" CG TYR r 137 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR r 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR r 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR r 137 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR r 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR r 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR r 137 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 137 " -0.025 2.00e-02 2.50e+03 1.81e-02 6.56e+00 pdb=" CG TYR E 137 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR E 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR E 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 137 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR E 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 137 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 137 " -0.018 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2284 2.71 - 3.25: 39076 3.25 - 3.80: 72277 3.80 - 4.35: 92805 4.35 - 4.90: 144621 Nonbonded interactions: 351063 Sorted by model distance: nonbonded pdb=" NH2 ARG S 63 " pdb=" O HOH S 601 " model vdw 2.157 3.120 nonbonded pdb=" OD1 ASP H 91 " pdb=" O HOH H 301 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP B 91 " pdb=" O HOH B 601 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP r 91 " pdb=" O HOH r 601 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP 1 91 " pdb=" O HOH 1 301 " model vdw 2.241 3.040 ... (remaining 351058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain '1' and (resid 4 through 176 or resid 201)) selection = (chain '2' and (resid 4 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 176 or resid 500)) selection = (chain 'B' and (resid 4 through 176 or resid 500)) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid 4 through 176 or resid 201)) selection = (chain 'H' and (resid 4 through 176 or resid 201)) selection = chain 'I' selection = chain 'K' selection = (chain 'M' and (resid 4 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 176 or resid 500)) selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 1.300 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 78.360 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.290 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34776 Z= 0.208 Angle : 0.719 5.874 46848 Z= 0.413 Chirality : 0.052 0.236 4920 Planarity : 0.007 0.060 6192 Dihedral : 15.650 89.477 13032 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.49 % Allowed : 5.04 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.30 (0.13), residues: 4032 helix: 1.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.94 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP r 93 HIS 0.011 0.002 HIS O 128 PHE 0.028 0.004 PHE W 41 TYR 0.036 0.005 TYR E 137 ARG 0.013 0.003 ARG K 76 Details of bonding type rmsd hydrogen bonds : bond 0.06558 ( 2706) hydrogen bonds : angle 4.37837 ( 8118) covalent geometry : bond 0.00407 (34776) covalent geometry : angle 0.71912 (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 712 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 694 time to evaluate : 4.419 Fit side-chains REVERT: 1 124 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8042 (mmtt) REVERT: 2 124 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8047 (mmtt) REVERT: 4 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8040 (mmtt) REVERT: 6 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8027 (mmtt) REVERT: A 124 LYS cc_start: 0.8242 (mmtt) cc_final: 0.8033 (mmtt) REVERT: B 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8036 (mmtt) REVERT: E 124 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8033 (mmtt) REVERT: F 124 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8034 (mmtt) REVERT: G 124 LYS cc_start: 0.8244 (mmtt) cc_final: 0.8025 (mmtt) REVERT: H 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8034 (mmtt) REVERT: I 124 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8040 (mmtt) REVERT: K 124 LYS cc_start: 0.8247 (mmtt) cc_final: 0.8037 (mmtt) REVERT: M 70 MET cc_start: 0.9008 (mtp) cc_final: 0.8703 (mtp) REVERT: M 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8031 (mmtt) REVERT: O 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8039 (mmtt) REVERT: P 124 LYS cc_start: 0.8255 (mmtt) cc_final: 0.8043 (mmtt) REVERT: Q 124 LYS cc_start: 0.8241 (mmtt) cc_final: 0.8023 (mmtt) REVERT: S 124 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8042 (mmtt) REVERT: U 124 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8043 (mmtt) REVERT: W 124 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8032 (mmtt) REVERT: X 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8040 (mmtt) REVERT: Y 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8039 (mmtt) REVERT: a 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8030 (mmtt) REVERT: e 124 LYS cc_start: 0.8245 (mmtt) cc_final: 0.8038 (mmtt) REVERT: r 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8038 (mmtt) outliers start: 18 outliers final: 18 residues processed: 712 average time/residue: 3.1817 time to fit residues: 2549.6666 Evaluate side-chains 574 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 556 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN I 136 HIS K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.143150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.138904 restraints weight = 18212.768| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 0.22 r_work: 0.3237 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work: 0.2905 rms_B_bonded: 3.27 restraints_weight: 0.1250 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0773 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= 0.157 Angle : 0.607 6.046 46848 Z= 0.340 Chirality : 0.041 0.160 4920 Planarity : 0.004 0.024 6192 Dihedral : 5.417 46.621 4572 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.49 % Allowed : 5.34 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.13), residues: 4032 helix: 3.15 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.85 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 2 93 HIS 0.006 0.001 HIS H 128 PHE 0.024 0.003 PHE P 41 TYR 0.027 0.003 TYR Q 39 ARG 0.003 0.001 ARG K 43 Details of bonding type rmsd hydrogen bonds : bond 0.05393 ( 2706) hydrogen bonds : angle 3.92214 ( 8118) covalent geometry : bond 0.00304 (34776) covalent geometry : angle 0.60731 (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 638 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 620 time to evaluate : 4.938 Fit side-chains REVERT: M 70 MET cc_start: 0.9138 (mtp) cc_final: 0.8854 (mtp) outliers start: 18 outliers final: 18 residues processed: 638 average time/residue: 2.3117 time to fit residues: 1671.5842 Evaluate side-chains 619 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 601 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 89 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 chunk 217 optimal weight: 0.9990 chunk 301 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 60 HIS G 109 ASN H 109 ASN I 109 ASN K 60 HIS K 109 ASN M 109 ASN O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 109 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.141944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.137673 restraints weight = 18367.744| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 0.22 r_work: 0.3222 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 1.15 restraints_weight: 0.2500 r_work: 0.2886 rms_B_bonded: 3.32 restraints_weight: 0.1250 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 34776 Z= 0.180 Angle : 0.638 6.189 46848 Z= 0.358 Chirality : 0.041 0.162 4920 Planarity : 0.004 0.029 6192 Dihedral : 5.481 47.474 4572 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.03 % Allowed : 4.36 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.13 (0.13), residues: 4032 helix: 3.14 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.77 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 93 HIS 0.004 0.001 HIS X 128 PHE 0.026 0.004 PHE 1 41 TYR 0.028 0.003 TYR H 39 ARG 0.004 0.001 ARG S 63 Details of bonding type rmsd hydrogen bonds : bond 0.05727 ( 2706) hydrogen bonds : angle 3.99420 ( 8118) covalent geometry : bond 0.00354 (34776) covalent geometry : angle 0.63782 (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 653 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 615 time to evaluate : 4.259 Fit side-chains outliers start: 38 outliers final: 18 residues processed: 633 average time/residue: 2.4501 time to fit residues: 1753.3858 Evaluate side-chains 617 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 599 time to evaluate : 4.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 289 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 363 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 339 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 60 HIS G 109 ASN H 109 ASN I 109 ASN K 60 HIS K 109 ASN M 109 ASN O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 109 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.144412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.140192 restraints weight = 18232.265| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 0.23 r_work: 0.3257 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2925 rms_B_bonded: 3.27 restraints_weight: 0.1250 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34776 Z= 0.136 Angle : 0.551 5.448 46848 Z= 0.308 Chirality : 0.038 0.146 4920 Planarity : 0.003 0.020 6192 Dihedral : 5.381 46.360 4572 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.68 % Allowed : 4.28 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.13), residues: 4032 helix: 3.41 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.72 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 6 93 HIS 0.004 0.001 HIS 4 128 PHE 0.021 0.003 PHE W 41 TYR 0.023 0.002 TYR H 39 ARG 0.003 0.000 ARG S 63 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 2706) hydrogen bonds : angle 3.78608 ( 8118) covalent geometry : bond 0.00259 (34776) covalent geometry : angle 0.55080 (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 653 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 628 time to evaluate : 4.264 Fit side-chains outliers start: 25 outliers final: 25 residues processed: 649 average time/residue: 2.4366 time to fit residues: 1803.3901 Evaluate side-chains 626 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 601 time to evaluate : 6.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 332 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 392 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 34 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN H 136 HIS I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN W 136 HIS X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN Y 136 HIS a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.141899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.137597 restraints weight = 18236.552| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 0.22 r_work: 0.3223 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.2886 rms_B_bonded: 3.36 restraints_weight: 0.1250 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 34776 Z= 0.190 Angle : 0.643 5.910 46848 Z= 0.361 Chirality : 0.041 0.163 4920 Planarity : 0.004 0.030 6192 Dihedral : 5.503 47.717 4572 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.84 % Allowed : 5.20 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.10 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.75 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP 6 93 HIS 0.004 0.001 HIS X 57 PHE 0.026 0.004 PHE F 41 TYR 0.028 0.003 TYR H 39 ARG 0.003 0.001 ARG P 43 Details of bonding type rmsd hydrogen bonds : bond 0.05830 ( 2706) hydrogen bonds : angle 4.01206 ( 8118) covalent geometry : bond 0.00376 (34776) covalent geometry : angle 0.64268 (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 656 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 625 time to evaluate : 4.384 Fit side-chains outliers start: 31 outliers final: 28 residues processed: 649 average time/residue: 2.3262 time to fit residues: 1712.9221 Evaluate side-chains 629 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 601 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 55 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 320 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 407 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 318 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 1 136 HIS 2 60 HIS 2 109 ASN 2 136 HIS 4 60 HIS 4 109 ASN 4 136 HIS 6 60 HIS 6 109 ASN 6 136 HIS A 60 HIS A 109 ASN A 136 HIS B 60 HIS B 109 ASN B 136 HIS E 60 HIS E 109 ASN E 136 HIS F 60 HIS F 109 ASN G 60 HIS G 109 ASN G 136 HIS H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN K 136 HIS M 60 HIS M 109 ASN M 136 HIS O 60 HIS O 109 ASN O 136 HIS P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN Q 136 HIS S 60 HIS S 109 ASN S 136 HIS U 60 HIS U 109 ASN U 136 HIS W 60 HIS W 109 ASN X 60 HIS X 109 ASN X 136 HIS Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN a 136 HIS e 60 HIS e 109 ASN e 136 HIS r 60 HIS r 109 ASN r 136 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.146847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.142658 restraints weight = 18168.192| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.22 r_work: 0.3293 rms_B_bonded: 0.56 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work: 0.2961 rms_B_bonded: 3.24 restraints_weight: 0.1250 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 34776 Z= 0.115 Angle : 0.505 5.318 46848 Z= 0.282 Chirality : 0.036 0.142 4920 Planarity : 0.003 0.020 6192 Dihedral : 5.276 44.993 4572 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.20 % Allowed : 4.85 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.75 (0.13), residues: 4032 helix: 3.63 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.66 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 6 93 HIS 0.003 0.001 HIS A 128 PHE 0.016 0.002 PHE H 41 TYR 0.021 0.002 TYR H 39 ARG 0.003 0.000 ARG S 63 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 2706) hydrogen bonds : angle 3.63847 ( 8118) covalent geometry : bond 0.00212 (34776) covalent geometry : angle 0.50526 (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 669 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 625 time to evaluate : 3.983 Fit side-chains outliers start: 44 outliers final: 9 residues processed: 649 average time/residue: 2.2505 time to fit residues: 1658.2883 Evaluate side-chains 682 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 673 time to evaluate : 4.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 34 optimal weight: 30.0000 chunk 235 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 328 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN F 136 HIS G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN P 136 HIS Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.141384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.137091 restraints weight = 18244.102| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 0.22 r_work: 0.3217 rms_B_bonded: 0.59 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 1.18 restraints_weight: 0.2500 r_work: 0.2879 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 34776 Z= 0.226 Angle : 0.699 6.050 46848 Z= 0.392 Chirality : 0.044 0.165 4920 Planarity : 0.005 0.034 6192 Dihedral : 4.618 22.098 4536 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.33 % Allowed : 6.24 % Favored : 92.43 % 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: 3.96 (0.13), residues: 4032 helix: 3.01 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP 6 93 HIS 0.005 0.002 HIS S 57 PHE 0.028 0.005 PHE G 41 TYR 0.032 0.004 TYR H 39 ARG 0.004 0.001 ARG W 43 Details of bonding type rmsd hydrogen bonds : bond 0.06179 ( 2706) hydrogen bonds : angle 4.09483 ( 8118) covalent geometry : bond 0.00453 (34776) covalent geometry : angle 0.69925 (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 730 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 681 time to evaluate : 4.198 Fit side-chains outliers start: 49 outliers final: 31 residues processed: 705 average time/residue: 2.3186 time to fit residues: 1853.6224 Evaluate side-chains 616 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 585 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 170 optimal weight: 20.0000 chunk 339 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.147823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.143635 restraints weight = 18168.980| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.22 r_work: 0.3309 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work: 0.2974 rms_B_bonded: 3.27 restraints_weight: 0.1250 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 34776 Z= 0.111 Angle : 0.507 5.216 46848 Z= 0.278 Chirality : 0.036 0.142 4920 Planarity : 0.003 0.020 6192 Dihedral : 4.454 22.678 4536 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.84 % Allowed : 7.08 % Favored : 92.08 % 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: 4.79 (0.13), residues: 4032 helix: 3.66 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.60 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 6 93 HIS 0.003 0.001 HIS P 128 PHE 0.015 0.002 PHE 1 41 TYR 0.020 0.002 TYR Q 39 ARG 0.001 0.000 ARG S 63 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 2706) hydrogen bonds : angle 3.59547 ( 8118) covalent geometry : bond 0.00203 (34776) covalent geometry : angle 0.50659 (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 627 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 596 time to evaluate : 3.884 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 620 average time/residue: 2.2385 time to fit residues: 1578.4944 Evaluate side-chains 584 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 572 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 400 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 328 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 397 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 278 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.142007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.137713 restraints weight = 18249.817| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 0.22 r_work: 0.3224 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.2887 rms_B_bonded: 3.32 restraints_weight: 0.1250 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34776 Z= 0.206 Angle : 0.671 5.923 46848 Z= 0.376 Chirality : 0.042 0.162 4920 Planarity : 0.004 0.031 6192 Dihedral : 4.596 22.645 4536 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.63 % Allowed : 7.16 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.13), residues: 4032 helix: 3.12 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP 6 93 HIS 0.005 0.002 HIS r 57 PHE 0.027 0.004 PHE P 41 TYR 0.031 0.003 TYR H 39 ARG 0.004 0.001 ARG 2 43 Details of bonding type rmsd hydrogen bonds : bond 0.05957 ( 2706) hydrogen bonds : angle 4.01814 ( 8118) covalent geometry : bond 0.00415 (34776) covalent geometry : angle 0.67128 (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 637 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 614 time to evaluate : 4.518 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 620 average time/residue: 2.2954 time to fit residues: 1616.1285 Evaluate side-chains 584 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 572 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 304 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 309 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.143290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.139108 restraints weight = 18108.542| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.22 r_work: 0.3243 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2909 rms_B_bonded: 3.25 restraints_weight: 0.1250 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34776 Z= 0.168 Angle : 0.613 5.722 46848 Z= 0.343 Chirality : 0.039 0.152 4920 Planarity : 0.004 0.025 6192 Dihedral : 4.601 22.677 4536 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.35 % Allowed : 7.43 % Favored : 92.21 % 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: 4.16 (0.13), residues: 4032 helix: 3.16 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 6 93 HIS 0.004 0.001 HIS M 57 PHE 0.025 0.003 PHE O 41 TYR 0.027 0.003 TYR H 39 ARG 0.002 0.001 ARG r 43 Details of bonding type rmsd hydrogen bonds : bond 0.05501 ( 2706) hydrogen bonds : angle 3.90624 ( 8118) covalent geometry : bond 0.00333 (34776) covalent geometry : angle 0.61287 (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 627 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 614 time to evaluate : 4.091 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 620 average time/residue: 2.3553 time to fit residues: 1676.0594 Evaluate side-chains 585 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 572 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 214 optimal weight: 9.9990 chunk 290 optimal weight: 7.9990 chunk 334 optimal weight: 20.0000 chunk 312 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 342 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 384 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.140857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.136584 restraints weight = 18343.483| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.21 r_work: 0.3208 rms_B_bonded: 0.59 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work: 0.2870 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 34776 Z= 0.271 Angle : 0.768 6.360 46848 Z= 0.432 Chirality : 0.046 0.171 4920 Planarity : 0.005 0.041 6192 Dihedral : 4.669 21.832 4536 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.82 % Allowed : 7.46 % Favored : 91.72 % 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: 3.44 (0.13), residues: 4032 helix: 2.64 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.60 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP M 93 HIS 0.006 0.002 HIS S 57 PHE 0.032 0.005 PHE O 41 TYR 0.034 0.004 TYR P 39 ARG 0.006 0.001 ARG K 43 Details of bonding type rmsd hydrogen bonds : bond 0.06592 ( 2706) hydrogen bonds : angle 4.23332 ( 8118) covalent geometry : bond 0.00546 (34776) covalent geometry : angle 0.76827 (46848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46017.83 seconds wall clock time: 793 minutes 44.50 seconds (47624.50 seconds total)