Starting phenix.real_space_refine on Tue Aug 26 06:52:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cps_16784/08_2025/8cps_16784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cps_16784/08_2025/8cps_16784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cps_16784/08_2025/8cps_16784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cps_16784/08_2025/8cps_16784.map" model { file = "/net/cci-nas-00/data/ceres_data/8cps_16784/08_2025/8cps_16784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cps_16784/08_2025/8cps_16784.cif" } resolution = 1.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 8540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36034 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "2" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "4" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "6" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} 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: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "Q" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "S" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "W" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} 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: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "a" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "e" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "r" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Time building chain proxies: 9.01, per 1000 atoms: 0.25 Number of scatterers: 36034 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 8540 8.00 N 5976 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 77 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 163 through 174 Processing helix chain '2' and resid 13 through 42 Processing helix chain '2' and resid 48 through 77 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 163 through 174 Processing helix chain '4' and resid 13 through 42 Processing helix chain '4' and resid 48 through 77 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 163 through 174 Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 48 through 76 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 163 through 174 Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 77 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 Processing helix chain 'a' and resid 13 through 42 Processing helix chain 'a' and resid 48 through 76 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 163 through 174 Processing helix chain 'e' and resid 13 through 42 Processing helix chain 'e' and resid 48 through 77 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 163 through 174 Processing helix chain 'r' and resid 13 through 42 Processing helix chain 'r' and resid 48 through 77 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 163 through 174 2706 hydrogen bonds defined for protein. 8118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11664 1.34 - 1.46: 5786 1.46 - 1.58: 17062 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX O 90 " pdb=" SG CSX O 90 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CSX e 90 " pdb=" SG CSX e 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CB CSX 6 90 " pdb=" SG CSX 6 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 44796 1.35 - 2.70: 1626 2.70 - 4.04: 281 4.04 - 5.39: 121 5.39 - 6.74: 24 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR E 39 " pdb=" CB TYR E 39 " pdb=" CG TYR E 39 " ideal model delta sigma weight residual 113.90 108.70 5.20 1.80e+00 3.09e-01 8.35e+00 angle pdb=" CA TYR I 39 " pdb=" CB TYR I 39 " pdb=" CG TYR I 39 " ideal model delta sigma weight residual 113.90 108.72 5.18 1.80e+00 3.09e-01 8.28e+00 angle pdb=" CA TYR 1 39 " pdb=" CB TYR 1 39 " pdb=" CG TYR 1 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" CA TYR Q 39 " pdb=" CB TYR Q 39 " pdb=" CG TYR Q 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" CA TYR M 39 " pdb=" CB TYR M 39 " pdb=" CG TYR M 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 19184 17.67 - 35.34: 1270 35.34 - 53.02: 323 53.02 - 70.69: 86 70.69 - 88.36: 137 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA VAL X 46 " pdb=" C VAL X 46 " pdb=" N ALA X 47 " pdb=" CA ALA X 47 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA VAL Q 46 " pdb=" C VAL Q 46 " pdb=" N ALA Q 47 " pdb=" CA ALA Q 47 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3644 0.043 - 0.085: 923 0.085 - 0.128: 252 0.128 - 0.171: 59 0.171 - 0.213: 42 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR K 137 " pdb=" N TYR K 137 " pdb=" C TYR K 137 " pdb=" CB TYR K 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA TYR O 137 " pdb=" N TYR O 137 " pdb=" C TYR O 137 " pdb=" CB TYR O 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA TYR P 137 " pdb=" N TYR P 137 " pdb=" C TYR P 137 " pdb=" CB TYR P 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 137 " -0.022 2.00e-02 2.50e+03 1.55e-02 4.81e+00 pdb=" CG TYR H 137 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR H 137 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 137 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR H 137 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR H 137 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Y 137 " 0.022 2.00e-02 2.50e+03 1.55e-02 4.80e+00 pdb=" CG TYR Y 137 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR Y 137 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR Y 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR Y 137 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR Y 137 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Y 137 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR Y 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 137 " -0.022 2.00e-02 2.50e+03 1.55e-02 4.78e+00 pdb=" CG TYR B 137 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 137 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 137 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 137 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 137 " -0.018 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1707 2.67 - 3.23: 37105 3.23 - 3.79: 69892 3.79 - 4.34: 94158 4.34 - 4.90: 146205 Nonbonded interactions: 349067 Sorted by model distance: nonbonded pdb=" OD1 ASP 1 123 " pdb=" O HOH 1 301 " model vdw 2.116 3.040 nonbonded pdb=" OD1 ASP e 123 " pdb=" O HOH e 601 " model vdw 2.116 3.040 nonbonded pdb=" OD1 ASP B 123 " pdb=" O HOH B 601 " model vdw 2.117 3.040 nonbonded pdb=" OD1 ASP A 123 " pdb=" O HOH A 601 " model vdw 2.117 3.040 nonbonded pdb=" OD1 ASP O 123 " pdb=" O HOH O 601 " model vdw 2.117 3.040 ... (remaining 349062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain '1' and resid 4 through 176) selection = (chain '2' and resid 4 through 176) selection = (chain '4' and resid 4 through 176) selection = (chain '6' and resid 4 through 176) selection = (chain 'A' and resid 4 through 176) selection = (chain 'B' and resid 4 through 176) selection = (chain 'E' and resid 4 through 176) selection = (chain 'F' and resid 4 through 176) selection = (chain 'G' and resid 4 through 176) selection = (chain 'H' and resid 4 through 176) selection = (chain 'I' and resid 4 through 176) selection = (chain 'K' and resid 4 through 176) selection = (chain 'M' and resid 4 through 176) selection = (chain 'O' and resid 4 through 176) selection = (chain 'P' and resid 4 through 176) selection = (chain 'Q' and resid 4 through 176) selection = (chain 'S' and resid 4 through 176) selection = (chain 'U' and resid 4 through 176) selection = (chain 'W' and resid 4 through 176) selection = (chain 'X' and resid 4 through 176) selection = (chain 'Y' and resid 4 through 176) selection = (chain 'a' and resid 4 through 176) selection = (chain 'e' and resid 4 through 176) selection = (chain 'r' and resid 4 through 176) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.810 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.960 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.003 0.073 34776 Z= 0.178 Angle : 0.660 6.742 46848 Z= 0.373 Chirality : 0.045 0.213 4920 Planarity : 0.006 0.055 6192 Dihedral : 15.421 88.361 13032 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.13), residues: 4032 helix: 1.70 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.94 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG r 76 TYR 0.029 0.004 TYR B 137 PHE 0.021 0.003 PHE I 41 TRP 0.012 0.002 TRP F 93 HIS 0.009 0.002 HIS F 128 Details of bonding type rmsd covalent geometry : bond 0.00339 (34776) covalent geometry : angle 0.65962 (46848) hydrogen bonds : bond 0.06325 ( 2706) hydrogen bonds : angle 4.26205 ( 8118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 738 time to evaluate : 1.220 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 738 average time/residue: 0.9520 time to fit residues: 804.3204 Evaluate side-chains 684 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 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 83 GLN 1 105 HIS 1 139 ASN 2 60 HIS 2 83 GLN 2 105 HIS 2 139 ASN 4 60 HIS 4 83 GLN 4 105 HIS 4 139 ASN 6 60 HIS 6 83 GLN 6 105 HIS 6 139 ASN A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS E 139 ASN F 83 GLN F 105 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS H 139 ASN I 83 GLN I 105 HIS I 139 ASN K 60 HIS K 83 GLN K 105 HIS K 139 ASN M 83 GLN M 105 HIS M 139 ASN M 141 GLN O 83 GLN O 105 HIS O 139 ASN P 83 GLN P 105 HIS P 139 ASN Q 83 GLN Q 105 HIS Q 141 GLN S 83 GLN S 105 HIS U 60 HIS U 83 GLN U 105 HIS U 139 ASN W 83 GLN W 105 HIS X 83 GLN X 105 HIS X 139 ASN Y 83 GLN Y 105 HIS Y 139 ASN a 83 GLN a 105 HIS e 83 GLN e 105 HIS e 139 ASN r 83 GLN r 105 HIS r 139 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.154474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.147712 restraints weight = 20305.123| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 0.31 r_work: 0.3240 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2884 rms_B_bonded: 3.43 restraints_weight: 0.1250 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 34776 Z= 0.239 Angle : 0.747 6.817 46848 Z= 0.410 Chirality : 0.047 0.161 4920 Planarity : 0.005 0.056 6192 Dihedral : 5.463 38.539 4536 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.97 (0.13), residues: 4032 helix: 2.92 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.29 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 2 63 TYR 0.030 0.005 TYR O 39 PHE 0.030 0.005 PHE A 41 TRP 0.007 0.002 TRP a 93 HIS 0.007 0.002 HIS F 128 Details of bonding type rmsd covalent geometry : bond 0.00486 (34776) covalent geometry : angle 0.74741 (46848) hydrogen bonds : bond 0.06335 ( 2706) hydrogen bonds : angle 4.08644 ( 8118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 699 time to evaluate : 1.508 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 699 average time/residue: 1.0587 time to fit residues: 846.4030 Evaluate side-chains 690 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 689 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 180 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 289 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 361 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 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 83 GLN 2 83 GLN 2 105 HIS 4 60 HIS 4 83 GLN 4 105 HIS 6 60 HIS 6 83 GLN 6 105 HIS A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN F 83 GLN F 105 HIS G 60 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS I 83 GLN K 60 HIS K 83 GLN M 83 GLN M 105 HIS O 83 GLN P 83 GLN P 105 HIS Q 83 GLN Q 105 HIS S 83 GLN S 105 HIS U 60 HIS U 83 GLN W 83 GLN W 105 HIS X 83 GLN Y 83 GLN Y 105 HIS a 83 GLN a 105 HIS e 83 GLN r 83 GLN r 105 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.154859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.147997 restraints weight = 20268.008| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 0.31 r_work: 0.3243 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2885 rms_B_bonded: 3.49 restraints_weight: 0.1250 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 34776 Z= 0.239 Angle : 0.741 7.098 46848 Z= 0.407 Chirality : 0.045 0.151 4920 Planarity : 0.005 0.056 6192 Dihedral : 5.393 37.536 4536 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.16 (0.13), residues: 4032 helix: 2.99 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.68 (0.30), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG M 63 TYR 0.030 0.004 TYR 2 39 PHE 0.028 0.005 PHE r 41 TRP 0.007 0.002 TRP 6 93 HIS 0.006 0.002 HIS X 128 Details of bonding type rmsd covalent geometry : bond 0.00485 (34776) covalent geometry : angle 0.74066 (46848) hydrogen bonds : bond 0.06328 ( 2706) hydrogen bonds : angle 4.08888 ( 8118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 713 time to evaluate : 1.564 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 713 average time/residue: 1.0616 time to fit residues: 866.5891 Evaluate side-chains 675 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 674 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 75 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 406 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 340 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 352 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 136 HIS 2 83 GLN 4 83 GLN 4 136 HIS 6 83 GLN A 83 GLN A 136 HIS B 83 GLN B 136 HIS E 83 GLN E 136 HIS F 83 GLN F 136 HIS G 83 GLN H 83 GLN I 83 GLN I 136 HIS K 83 GLN K 136 HIS M 83 GLN O 83 GLN O 136 HIS P 83 GLN Q 83 GLN S 83 GLN S 136 HIS U 83 GLN U 136 HIS W 83 GLN X 83 GLN X 136 HIS Y 83 GLN a 83 GLN e 83 GLN e 136 HIS r 83 GLN r 136 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.158080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.151267 restraints weight = 20031.516| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 0.31 r_work: 0.3285 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2929 rms_B_bonded: 3.51 restraints_weight: 0.1250 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34776 Z= 0.143 Angle : 0.590 6.421 46848 Z= 0.320 Chirality : 0.039 0.138 4920 Planarity : 0.003 0.044 6192 Dihedral : 4.876 26.009 4536 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.90 (0.13), residues: 4032 helix: 3.56 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.61 (0.30), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 63 TYR 0.023 0.003 TYR O 39 PHE 0.018 0.003 PHE 1 41 TRP 0.008 0.002 TRP 2 93 HIS 0.004 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00278 (34776) covalent geometry : angle 0.58985 (46848) hydrogen bonds : bond 0.05180 ( 2706) hydrogen bonds : angle 3.72680 ( 8118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 703 time to evaluate : 1.568 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 703 average time/residue: 1.0797 time to fit residues: 867.2742 Evaluate side-chains 690 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 689 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 60 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 299 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 268 optimal weight: 0.9990 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 83 GLN 1 105 HIS 2 83 GLN 2 105 HIS 4 83 GLN 4 105 HIS 6 83 GLN 6 105 HIS 6 136 HIS A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS F 83 GLN F 105 HIS G 83 GLN G 105 HIS G 136 HIS H 83 GLN H 105 HIS I 60 HIS I 83 GLN I 105 HIS K 83 GLN K 105 HIS M 83 GLN M 105 HIS M 136 HIS O 83 GLN O 105 HIS P 83 GLN P 105 HIS Q 60 HIS Q 83 GLN Q 105 HIS Q 136 HIS S 83 GLN S 105 HIS U 83 GLN U 105 HIS W 83 GLN W 105 HIS W 136 HIS X 83 GLN X 105 HIS Y 83 GLN Y 105 HIS a 83 GLN a 105 HIS a 136 HIS e 83 GLN e 105 HIS r 83 GLN r 105 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.155233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.148412 restraints weight = 20159.506| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.31 r_work: 0.3251 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2891 rms_B_bonded: 3.47 restraints_weight: 0.1250 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 34776 Z= 0.238 Angle : 0.735 7.011 46848 Z= 0.404 Chirality : 0.045 0.157 4920 Planarity : 0.004 0.046 6192 Dihedral : 5.286 35.258 4536 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.08 % Allowed : 5.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.37 (0.13), residues: 4032 helix: 3.12 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.81 (0.31), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG E 63 TYR 0.030 0.004 TYR a 39 PHE 0.027 0.005 PHE 6 41 TRP 0.006 0.002 TRP Q 93 HIS 0.005 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00483 (34776) covalent geometry : angle 0.73483 (46848) hydrogen bonds : bond 0.06288 ( 2706) hydrogen bonds : angle 4.04592 ( 8118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 681 time to evaluate : 1.621 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 681 average time/residue: 1.0802 time to fit residues: 840.5433 Evaluate side-chains 658 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 657 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 356 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 404 optimal weight: 5.9990 chunk 392 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 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 83 GLN 1 105 HIS 2 83 GLN 2 105 HIS 4 83 GLN 4 105 HIS 6 83 GLN 6 105 HIS A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS F 83 GLN F 105 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS I 83 GLN I 105 HIS K 83 GLN K 105 HIS M 83 GLN M 105 HIS O 83 GLN O 105 HIS P 83 GLN P 105 HIS Q 83 GLN Q 105 HIS S 83 GLN S 105 HIS U 83 GLN U 105 HIS W 83 GLN W 105 HIS X 83 GLN X 105 HIS Y 83 GLN Y 105 HIS a 83 GLN a 105 HIS e 83 GLN e 105 HIS r 83 GLN r 105 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.157606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.150725 restraints weight = 20131.438| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 0.32 r_work: 0.3281 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2920 rms_B_bonded: 3.53 restraints_weight: 0.1250 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34776 Z= 0.156 Angle : 0.608 6.441 46848 Z= 0.332 Chirality : 0.039 0.138 4920 Planarity : 0.004 0.044 6192 Dihedral : 4.917 26.669 4536 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.87 (0.13), residues: 4032 helix: 3.53 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.67 (0.30), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 63 TYR 0.025 0.003 TYR 1 39 PHE 0.020 0.003 PHE Q 41 TRP 0.008 0.002 TRP G 93 HIS 0.004 0.001 HIS 2 128 Details of bonding type rmsd covalent geometry : bond 0.00305 (34776) covalent geometry : angle 0.60820 (46848) hydrogen bonds : bond 0.05355 ( 2706) hydrogen bonds : angle 3.76832 ( 8118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 689 time to evaluate : 1.509 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 689 average time/residue: 1.0019 time to fit residues: 788.7563 Evaluate side-chains 683 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 682 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 341 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 347 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 369 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 358 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 105 HIS 2 83 GLN 2 105 HIS 4 60 HIS 4 83 GLN 4 105 HIS 6 60 HIS 6 83 GLN 6 105 HIS A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS F 83 GLN F 105 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS I 60 HIS I 83 GLN I 105 HIS K 60 HIS K 83 GLN K 105 HIS M 83 GLN M 105 HIS O 83 GLN O 105 HIS P 83 GLN P 105 HIS Q 60 HIS Q 83 GLN Q 105 HIS S 83 GLN S 105 HIS U 60 HIS U 83 GLN U 105 HIS W 83 GLN W 105 HIS X 83 GLN X 105 HIS Y 83 GLN Y 105 HIS a 83 GLN a 105 HIS e 83 GLN e 105 HIS r 83 GLN r 105 HIS Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.155766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.149006 restraints weight = 20258.014| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 0.31 r_work: 0.3274 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.2914 rms_B_bonded: 3.13 restraints_weight: 0.1250 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34776 Z= 0.216 Angle : 0.707 6.774 46848 Z= 0.386 Chirality : 0.043 0.147 4920 Planarity : 0.004 0.044 6192 Dihedral : 5.176 32.002 4536 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.50 (0.13), residues: 4032 helix: 3.23 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.77 (0.31), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 63 TYR 0.029 0.004 TYR E 39 PHE 0.025 0.004 PHE B 41 TRP 0.006 0.002 TRP H 93 HIS 0.005 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00435 (34776) covalent geometry : angle 0.70671 (46848) hydrogen bonds : bond 0.06089 ( 2706) hydrogen bonds : angle 3.98283 ( 8118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 675 time to evaluate : 1.172 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 675 average time/residue: 0.9324 time to fit residues: 722.6821 Evaluate side-chains 672 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 671 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 354 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 277 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 105 HIS 2 83 GLN 2 105 HIS 4 83 GLN 4 105 HIS 6 83 GLN 6 105 HIS 6 136 HIS A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS F 83 GLN F 105 HIS G 83 GLN G 105 HIS G 136 HIS H 83 GLN H 105 HIS I 83 GLN I 105 HIS I 136 HIS K 83 GLN K 105 HIS M 83 GLN M 105 HIS M 136 HIS O 83 GLN O 105 HIS P 83 GLN P 105 HIS Q 83 GLN Q 105 HIS Q 136 HIS S 83 GLN S 105 HIS U 83 GLN U 105 HIS W 83 GLN W 105 HIS W 136 HIS X 83 GLN X 105 HIS Y 83 GLN Y 105 HIS a 83 GLN a 105 HIS a 136 HIS e 83 GLN e 105 HIS r 83 GLN r 105 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.158353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.151608 restraints weight = 20052.450| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 0.31 r_work: 0.3308 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2951 rms_B_bonded: 3.14 restraints_weight: 0.1250 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34776 Z= 0.143 Angle : 0.586 6.074 46848 Z= 0.319 Chirality : 0.039 0.136 4920 Planarity : 0.003 0.046 6192 Dihedral : 4.777 22.843 4536 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 6.37 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.00 (0.13), residues: 4032 helix: 3.63 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.67 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 63 TYR 0.024 0.003 TYR e 39 PHE 0.018 0.003 PHE Q 41 TRP 0.008 0.002 TRP U 93 HIS 0.003 0.001 HIS M 128 Details of bonding type rmsd covalent geometry : bond 0.00278 (34776) covalent geometry : angle 0.58580 (46848) hydrogen bonds : bond 0.05143 ( 2706) hydrogen bonds : angle 3.70744 ( 8118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 693 time to evaluate : 1.229 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 693 average time/residue: 0.9694 time to fit residues: 770.1215 Evaluate side-chains 674 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 673 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 378 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 387 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 195 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 368 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 105 HIS 2 60 HIS 2 83 GLN 2 105 HIS 4 60 HIS 4 83 GLN 4 105 HIS 6 60 HIS 6 83 GLN 6 105 HIS A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS F 83 GLN F 105 HIS G 60 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS I 60 HIS I 83 GLN I 105 HIS K 60 HIS K 83 GLN K 105 HIS M 83 GLN M 105 HIS O 83 GLN O 105 HIS P 83 GLN P 105 HIS Q 60 HIS Q 83 GLN Q 105 HIS S 83 GLN S 105 HIS U 60 HIS U 83 GLN U 105 HIS W 83 GLN W 105 HIS X 83 GLN X 105 HIS Y 83 GLN Y 105 HIS a 83 GLN a 105 HIS e 83 GLN e 105 HIS r 83 GLN r 105 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.157960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.151232 restraints weight = 20024.800| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 0.32 r_work: 0.3304 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2948 rms_B_bonded: 3.13 restraints_weight: 0.1250 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34776 Z= 0.151 Angle : 0.606 6.123 46848 Z= 0.329 Chirality : 0.039 0.137 4920 Planarity : 0.004 0.048 6192 Dihedral : 4.776 23.012 4536 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.91 (0.13), residues: 4032 helix: 3.57 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.62 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 63 TYR 0.024 0.003 TYR A 39 PHE 0.018 0.003 PHE P 41 TRP 0.008 0.002 TRP P 93 HIS 0.004 0.001 HIS M 136 Details of bonding type rmsd covalent geometry : bond 0.00294 (34776) covalent geometry : angle 0.60561 (46848) hydrogen bonds : bond 0.05264 ( 2706) hydrogen bonds : angle 3.75166 ( 8118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 1.549 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 678 average time/residue: 1.0742 time to fit residues: 832.2206 Evaluate side-chains 688 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 687 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 34 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 286 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 105 HIS 2 83 GLN 2 105 HIS 4 83 GLN 4 105 HIS 6 83 GLN 6 105 HIS A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS F 83 GLN F 105 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS I 83 GLN I 105 HIS K 83 GLN K 105 HIS M 83 GLN M 105 HIS O 83 GLN O 105 HIS P 83 GLN P 105 HIS Q 83 GLN Q 105 HIS S 83 GLN S 105 HIS U 83 GLN U 105 HIS W 83 GLN W 105 HIS X 83 GLN X 105 HIS Y 83 GLN Y 105 HIS a 83 GLN a 105 HIS e 83 GLN e 105 HIS r 83 GLN r 105 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.156572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.149808 restraints weight = 20215.780| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.32 r_work: 0.3287 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2928 rms_B_bonded: 3.13 restraints_weight: 0.1250 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34776 Z= 0.188 Angle : 0.670 6.469 46848 Z= 0.366 Chirality : 0.042 0.141 4920 Planarity : 0.004 0.049 6192 Dihedral : 4.927 25.690 4536 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 7.16 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.62 (0.13), residues: 4032 helix: 3.32 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.75 (0.30), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 63 TYR 0.027 0.003 TYR r 39 PHE 0.022 0.004 PHE Q 41 TRP 0.006 0.002 TRP a 93 HIS 0.005 0.001 HIS G 136 Details of bonding type rmsd covalent geometry : bond 0.00374 (34776) covalent geometry : angle 0.67008 (46848) hydrogen bonds : bond 0.05752 ( 2706) hydrogen bonds : angle 3.91236 ( 8118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 697 time to evaluate : 1.691 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 697 average time/residue: 1.0917 time to fit residues: 869.0597 Evaluate side-chains 689 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 688 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 185 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 354 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 chunk 314 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 105 HIS 2 83 GLN 4 83 GLN 4 105 HIS 6 83 GLN 6 105 HIS A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 60 HIS E 83 GLN E 105 HIS F 83 GLN F 105 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS I 83 GLN I 105 HIS I 136 HIS K 83 GLN K 105 HIS M 83 GLN M 105 HIS O 83 GLN O 105 HIS P 83 GLN P 105 HIS Q 83 GLN S 83 GLN S 105 HIS U 83 GLN U 105 HIS W 60 HIS W 83 GLN W 105 HIS X 83 GLN X 105 HIS Y 83 GLN a 83 GLN e 83 GLN e 105 HIS r 83 GLN r 105 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.162479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.155778 restraints weight = 19848.528| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 0.31 r_work: 0.3365 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3014 rms_B_bonded: 3.15 restraints_weight: 0.1250 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 34776 Z= 0.113 Angle : 0.530 5.573 46848 Z= 0.286 Chirality : 0.036 0.134 4920 Planarity : 0.003 0.048 6192 Dihedral : 4.430 22.769 4536 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.03 % Allowed : 7.05 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.23 (0.13), residues: 4032 helix: 3.85 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.39 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 63 TYR 0.017 0.002 TYR A 39 PHE 0.012 0.002 PHE 2 41 TRP 0.009 0.002 TRP H 93 HIS 0.006 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00212 (34776) covalent geometry : angle 0.52985 (46848) hydrogen bonds : bond 0.04351 ( 2706) hydrogen bonds : angle 3.51570 ( 8118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22002.36 seconds wall clock time: 374 minutes 26.62 seconds (22466.62 seconds total)