Starting phenix.real_space_refine on Tue Aug 26 06:26:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpu_16786/08_2025/8cpu_16786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpu_16786/08_2025/8cpu_16786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cpu_16786/08_2025/8cpu_16786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpu_16786/08_2025/8cpu_16786.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpu_16786/08_2025/8cpu_16786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpu_16786/08_2025/8cpu_16786.cif" } resolution = 1.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 8329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s 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: 35823 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: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "2" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "4" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "6" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "F" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "H" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "K" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "M" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "O" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "P" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "Q" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "S" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "U" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "X" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "Y" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "a" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "e" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "r" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 6.58, per 1000 atoms: 0.18 Number of scatterers: 35823 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 8329 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: 3.18 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 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: 0.89 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: 5.79 Time building geometry restraints manager: 3.83 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: 5131 1.46 - 1.57: 17741 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB CSX S 90 " pdb=" SG CSX S 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB CSX U 90 " pdb=" SG CSX U 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB CSX 1 90 " pdb=" SG CSX 1 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB CSX 2 90 " pdb=" SG CSX 2 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 42883 1.11 - 2.23: 3162 2.23 - 3.34: 537 3.34 - 4.46: 182 4.46 - 5.57: 84 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR Q 39 " pdb=" CB TYR Q 39 " pdb=" CG TYR Q 39 " ideal model delta sigma weight residual 113.90 108.33 5.57 1.80e+00 3.09e-01 9.57e+00 angle pdb=" CA TYR 4 39 " pdb=" CB TYR 4 39 " pdb=" CG TYR 4 39 " ideal model delta sigma weight residual 113.90 108.37 5.53 1.80e+00 3.09e-01 9.45e+00 angle pdb=" CA TYR W 39 " pdb=" CB TYR W 39 " pdb=" CG TYR W 39 " ideal model delta sigma weight residual 113.90 108.38 5.52 1.80e+00 3.09e-01 9.41e+00 angle pdb=" CA TYR r 39 " pdb=" CB TYR r 39 " pdb=" CG TYR r 39 " ideal model delta sigma weight residual 113.90 108.40 5.50 1.80e+00 3.09e-01 9.34e+00 angle pdb=" CA TYR F 39 " pdb=" CB TYR F 39 " pdb=" CG TYR F 39 " ideal model delta sigma weight residual 113.90 108.40 5.50 1.80e+00 3.09e-01 9.34e+00 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 19241 17.84 - 35.67: 1256 35.67 - 53.51: 336 53.51 - 71.34: 69 71.34 - 89.18: 98 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA ASP S 44 " pdb=" CB ASP S 44 " pdb=" CG ASP S 44 " pdb=" OD1 ASP S 44 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP K 44 " pdb=" CB ASP K 44 " pdb=" CG ASP K 44 " pdb=" OD1 ASP K 44 " ideal model delta sinusoidal sigma weight residual -30.00 -87.39 57.39 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP X 44 " pdb=" CB ASP X 44 " pdb=" CG ASP X 44 " pdb=" OD1 ASP X 44 " ideal model delta sinusoidal sigma weight residual -30.00 -87.39 57.39 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3623 0.046 - 0.092: 930 0.092 - 0.138: 276 0.138 - 0.185: 49 0.185 - 0.231: 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 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA TYR e 137 " pdb=" N TYR e 137 " pdb=" C TYR e 137 " pdb=" CB TYR e 137 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+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 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 32 " 0.041 2.00e-02 2.50e+03 3.48e-02 2.43e+01 pdb=" CG TYR H 32 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR H 32 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR H 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR H 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 32 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR H 32 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR H 32 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 32 " 0.041 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR Q 32 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 32 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 32 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR Q 32 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR Q 32 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " -0.041 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR F 32 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " -0.003 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 1009 2.56 - 3.15: 30871 3.15 - 3.73: 67634 3.73 - 4.32: 93417 4.32 - 4.90: 148715 Nonbonded interactions: 341646 Sorted by model distance: nonbonded pdb=" OD1 ASP G 131 " pdb=" O HOH G 301 " model vdw 1.976 3.040 nonbonded pdb=" OD1 ASP 6 131 " pdb=" O HOH 6 301 " model vdw 1.993 3.040 nonbonded pdb=" O HOH G 301 " pdb=" O HOH W 601 " model vdw 2.021 3.040 nonbonded pdb=" OD1 ASP W 131 " pdb=" O HOH W 601 " model vdw 2.041 3.040 nonbonded pdb=" O HOH 6 301 " pdb=" O HOH W 601 " model vdw 2.050 3.040 ... (remaining 341641 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: 0.00 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: 1.490 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.020 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 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:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 0.072 34776 Z= 0.208 Angle : 0.707 5.569 46848 Z= 0.403 Chirality : 0.050 0.231 4920 Planarity : 0.007 0.057 6192 Dihedral : 14.912 89.177 13032 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: 2.29 (0.13), residues: 4032 helix: 1.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.88 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG F 76 TYR 0.085 0.007 TYR H 32 PHE 0.023 0.003 PHE A 41 TRP 0.009 0.002 TRP F 93 HIS 0.008 0.002 HIS P 128 Details of bonding type rmsd covalent geometry : bond 0.00415 (34776) covalent geometry : angle 0.70740 (46848) hydrogen bonds : bond 0.06845 ( 2706) hydrogen bonds : angle 4.38333 ( 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 610 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 1.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 0.8670 time to fit residues: 607.6554 Evaluate side-chains 571 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.150432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.143445 restraints weight = 18314.590| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 0.27 r_work: 0.3331 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.2965 rms_B_bonded: 2.99 restraints_weight: 0.1250 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34776 Z= 0.187 Angle : 0.638 5.748 46848 Z= 0.355 Chirality : 0.040 0.156 4920 Planarity : 0.004 0.027 6192 Dihedral : 4.523 21.420 4536 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.65 % Allowed : 2.67 % Favored : 96.68 % 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: 4.02 (0.13), residues: 4032 helix: 3.09 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.65 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 63 TYR 0.049 0.005 TYR 4 32 PHE 0.018 0.003 PHE 2 81 TRP 0.004 0.001 TRP K 93 HIS 0.005 0.002 HIS X 118 Details of bonding type rmsd covalent geometry : bond 0.00383 (34776) covalent geometry : angle 0.63832 (46848) hydrogen bonds : bond 0.06051 ( 2706) hydrogen bonds : angle 3.94498 ( 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 593 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 569 time to evaluate : 0.990 Fit side-chains REVERT: F 63 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7405 (ttm-80) REVERT: H 63 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7421 (ttm-80) REVERT: U 63 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7409 (ttm-80) REVERT: W 63 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7413 (ttm-80) REVERT: Y 63 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7414 (ttm-80) outliers start: 24 outliers final: 0 residues processed: 569 average time/residue: 0.9680 time to fit residues: 624.6280 Evaluate side-chains 558 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 292 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 351 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.150933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.144068 restraints weight = 18158.315| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 0.27 r_work: 0.3341 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.2977 rms_B_bonded: 2.93 restraints_weight: 0.1250 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34776 Z= 0.178 Angle : 0.622 6.110 46848 Z= 0.345 Chirality : 0.039 0.145 4920 Planarity : 0.004 0.041 6192 Dihedral : 4.451 21.622 4536 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 3.24 % Favored : 96.11 % 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: 4.13 (0.12), residues: 4032 helix: 3.16 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.69 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 63 TYR 0.030 0.004 TYR A 32 PHE 0.018 0.003 PHE 2 81 TRP 0.005 0.002 TRP r 93 HIS 0.005 0.002 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00363 (34776) covalent geometry : angle 0.62240 (46848) hydrogen bonds : bond 0.05934 ( 2706) hydrogen bonds : angle 3.86393 ( 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 599 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 575 time to evaluate : 1.357 Fit side-chains REVERT: F 63 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7403 (ttm-80) REVERT: H 63 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7410 (ttm-80) REVERT: P 63 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7392 (ttm-80) REVERT: U 63 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7404 (ttm-80) REVERT: W 63 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7402 (ttm-80) REVERT: Y 63 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7413 (ttm-80) outliers start: 24 outliers final: 19 residues processed: 575 average time/residue: 1.1168 time to fit residues: 725.4734 Evaluate side-chains 575 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 556 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain r residue 14 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 350 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.154460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.147475 restraints weight = 18271.172| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.27 r_work: 0.3388 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.3027 rms_B_bonded: 2.99 restraints_weight: 0.1250 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1245 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= 0.121 Angle : 0.504 4.851 46848 Z= 0.279 Chirality : 0.035 0.135 4920 Planarity : 0.003 0.029 6192 Dihedral : 4.271 21.798 4536 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.65 % Allowed : 3.08 % Favored : 96.27 % 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: 4.94 (0.13), residues: 4032 helix: 3.74 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.93 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 63 TYR 0.017 0.002 TYR 1 39 PHE 0.011 0.002 PHE a 132 TRP 0.008 0.002 TRP Q 93 HIS 0.003 0.001 HIS Y 128 Details of bonding type rmsd covalent geometry : bond 0.00228 (34776) covalent geometry : angle 0.50366 (46848) hydrogen bonds : bond 0.04851 ( 2706) hydrogen bonds : angle 3.55003 ( 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 643 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 619 time to evaluate : 1.573 Fit side-chains REVERT: 2 63 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7447 (ttm-80) REVERT: F 63 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7440 (ttt90) REVERT: H 63 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7439 (ttt90) REVERT: O 63 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7455 (ttm-80) REVERT: P 63 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.7363 (ttt90) REVERT: S 63 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7384 (ttt90) REVERT: U 63 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7404 (ttm-80) REVERT: W 63 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7383 (ttt90) REVERT: Y 63 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7430 (ttt90) outliers start: 24 outliers final: 0 residues processed: 619 average time/residue: 1.0070 time to fit residues: 709.5067 Evaluate side-chains 536 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 207 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 400 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 407 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 393 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 1 139 ASN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 4 139 ASN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN A 139 ASN B 86 GLN B 112 GLN B 139 ASN E 86 GLN E 139 ASN F 86 GLN F 109 ASN F 112 GLN F 139 ASN G 86 GLN G 139 ASN H 86 GLN I 86 GLN I 112 GLN I 139 ASN K 86 GLN K 112 GLN K 139 ASN M 86 GLN M 139 ASN O 86 GLN O 139 ASN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN S 139 ASN U 86 GLN W 86 GLN W 139 ASN X 86 GLN X 139 ASN Y 86 GLN Y 112 GLN a 86 GLN a 139 ASN e 86 GLN e 112 GLN e 139 ASN r 86 GLN r 112 GLN r 139 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.151474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.144449 restraints weight = 18140.157| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 0.27 r_work: 0.3347 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2979 rms_B_bonded: 2.99 restraints_weight: 0.1250 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34776 Z= 0.166 Angle : 0.594 5.510 46848 Z= 0.329 Chirality : 0.038 0.134 4920 Planarity : 0.004 0.038 6192 Dihedral : 4.429 22.491 4536 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.90 % Allowed : 3.95 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.35 (0.12), residues: 4032 helix: 3.32 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.75 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 63 TYR 0.023 0.003 TYR E 39 PHE 0.017 0.002 PHE e 81 TRP 0.005 0.001 TRP M 93 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00336 (34776) covalent geometry : angle 0.59354 (46848) hydrogen bonds : bond 0.05821 ( 2706) hydrogen bonds : angle 3.78680 ( 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 565 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 532 time to evaluate : 1.709 Fit side-chains REVERT: 2 63 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7429 (ttm-80) REVERT: 6 63 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7410 (ttm-80) REVERT: F 63 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7410 (ttm-80) REVERT: O 63 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7438 (ttm-80) REVERT: P 63 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7401 (ttm-80) REVERT: U 63 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7410 (ttm-80) REVERT: W 63 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7408 (ttt90) outliers start: 33 outliers final: 24 residues processed: 541 average time/residue: 1.0319 time to fit residues: 634.5576 Evaluate side-chains 540 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 516 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain r residue 14 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 385 optimal weight: 10.0000 chunk 364 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 1 139 ASN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN A 139 ASN B 86 GLN B 112 GLN B 139 ASN E 86 GLN E 139 ASN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN X 139 ASN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.151687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.144624 restraints weight = 18174.637| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 0.27 r_work: 0.3349 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2981 rms_B_bonded: 3.03 restraints_weight: 0.1250 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34776 Z= 0.162 Angle : 0.588 5.373 46848 Z= 0.326 Chirality : 0.037 0.139 4920 Planarity : 0.004 0.036 6192 Dihedral : 4.408 22.557 4536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.87 % Allowed : 4.30 % Favored : 94.83 % 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: 4.27 (0.12), residues: 4032 helix: 3.27 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.70 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 63 TYR 0.023 0.003 TYR Y 39 PHE 0.016 0.002 PHE Q 81 TRP 0.005 0.001 TRP W 93 HIS 0.004 0.001 HIS 2 118 Details of bonding type rmsd covalent geometry : bond 0.00325 (34776) covalent geometry : angle 0.58796 (46848) hydrogen bonds : bond 0.05715 ( 2706) hydrogen bonds : angle 3.76410 ( 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 555 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 523 time to evaluate : 1.388 Fit side-chains REVERT: 2 63 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7400 (ttt90) REVERT: 6 63 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7412 (ttm-80) REVERT: F 63 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7396 (ttm-80) REVERT: O 63 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7431 (ttm-80) REVERT: P 63 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7381 (ttm-80) REVERT: S 63 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7417 (ttm-80) REVERT: U 63 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7419 (ttm-80) REVERT: W 63 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7391 (ttt90) outliers start: 32 outliers final: 24 residues processed: 531 average time/residue: 1.0266 time to fit residues: 617.6485 Evaluate side-chains 535 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 511 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain r residue 14 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 137 optimal weight: 20.0000 chunk 402 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 144 optimal weight: 0.0770 chunk 7 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN W 139 ASN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.149853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.142751 restraints weight = 18210.707| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.27 r_work: 0.3323 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.2957 rms_B_bonded: 2.97 restraints_weight: 0.1250 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 34776 Z= 0.249 Angle : 0.747 6.362 46848 Z= 0.410 Chirality : 0.043 0.147 4920 Planarity : 0.005 0.047 6192 Dihedral : 4.564 22.296 4536 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.71 % Allowed : 4.96 % Favored : 94.34 % 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: 3.35 (0.12), residues: 4032 helix: 2.64 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.32 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 63 TYR 0.031 0.004 TYR H 39 PHE 0.023 0.003 PHE a 81 TRP 0.004 0.002 TRP S 93 HIS 0.007 0.002 HIS Y 65 Details of bonding type rmsd covalent geometry : bond 0.00523 (34776) covalent geometry : angle 0.74719 (46848) hydrogen bonds : bond 0.06701 ( 2706) hydrogen bonds : angle 4.04136 ( 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 575 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 549 time to evaluate : 1.506 Fit side-chains REVERT: 2 63 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7428 (ttm-80) REVERT: 6 63 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7418 (ttm-80) REVERT: O 63 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7431 (ttm-80) REVERT: P 63 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: S 63 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7412 (ttm-80) REVERT: U 63 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7426 (ttm-80) REVERT: W 63 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7425 (ttm-80) outliers start: 26 outliers final: 24 residues processed: 551 average time/residue: 1.0944 time to fit residues: 684.6105 Evaluate side-chains 563 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 539 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain r residue 14 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 313 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 395 optimal weight: 3.9990 chunk 351 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN W 139 ASN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.150063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.143004 restraints weight = 18171.459| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.27 r_work: 0.3327 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2960 rms_B_bonded: 2.97 restraints_weight: 0.1250 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 34776 Z= 0.250 Angle : 0.745 6.467 46848 Z= 0.410 Chirality : 0.043 0.148 4920 Planarity : 0.005 0.045 6192 Dihedral : 4.595 22.336 4536 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 5.01 % Favored : 94.34 % 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: 3.08 (0.12), residues: 4032 helix: 2.46 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.17 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 63 TYR 0.030 0.004 TYR O 39 PHE 0.024 0.004 PHE K 81 TRP 0.004 0.002 TRP A 93 HIS 0.007 0.002 HIS 1 65 Details of bonding type rmsd covalent geometry : bond 0.00528 (34776) covalent geometry : angle 0.74467 (46848) hydrogen bonds : bond 0.06631 ( 2706) hydrogen bonds : angle 4.06543 ( 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 547 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 523 time to evaluate : 1.336 Fit side-chains REVERT: 2 63 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7427 (ttm-80) REVERT: 6 63 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7416 (ttm-80) REVERT: H 63 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7448 (ttm-80) REVERT: O 63 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7435 (ttm-80) REVERT: P 63 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7409 (ttm-80) REVERT: S 63 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: U 63 ARG cc_start: 0.7827 (ttp-170) cc_final: 0.7440 (ttm-80) REVERT: W 63 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7427 (ttm-80) outliers start: 24 outliers final: 24 residues processed: 523 average time/residue: 1.0074 time to fit residues: 599.0257 Evaluate side-chains 552 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 528 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain r residue 14 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 238 optimal weight: 0.6980 chunk 222 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 chunk 335 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 398 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 329 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 369 optimal weight: 9.9990 chunk 342 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.151243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.144220 restraints weight = 18170.628| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 0.28 r_work: 0.3344 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2978 rms_B_bonded: 2.97 restraints_weight: 0.1250 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34776 Z= 0.186 Angle : 0.639 5.704 46848 Z= 0.353 Chirality : 0.039 0.143 4920 Planarity : 0.004 0.041 6192 Dihedral : 4.525 22.544 4536 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 5.17 % 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 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: 3.62 (0.12), residues: 4032 helix: 2.85 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.34 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 63 TYR 0.025 0.003 TYR Y 39 PHE 0.018 0.003 PHE E 81 TRP 0.006 0.002 TRP I 93 HIS 0.005 0.002 HIS 2 118 Details of bonding type rmsd covalent geometry : bond 0.00381 (34776) covalent geometry : angle 0.63900 (46848) hydrogen bonds : bond 0.06028 ( 2706) hydrogen bonds : angle 3.89591 ( 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 536 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 512 time to evaluate : 1.487 Fit side-chains REVERT: 2 63 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: 6 63 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7416 (ttm-80) REVERT: H 63 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7436 (ttm-80) REVERT: O 63 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7436 (ttm-80) REVERT: P 63 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7401 (ttm-80) REVERT: S 63 ARG cc_start: 0.7828 (ttp-170) cc_final: 0.7408 (ttm-80) REVERT: U 63 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7441 (ttm-80) REVERT: W 63 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7410 (ttm-80) REVERT: Y 63 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7425 (ttm-80) outliers start: 24 outliers final: 24 residues processed: 512 average time/residue: 1.0544 time to fit residues: 612.3512 Evaluate side-chains 527 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 503 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain r residue 14 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 80 optimal weight: 9.9990 chunk 378 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.152278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.145249 restraints weight = 18281.827| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 0.27 r_work: 0.3359 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.2992 rms_B_bonded: 3.01 restraints_weight: 0.1250 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34776 Z= 0.154 Angle : 0.585 5.298 46848 Z= 0.323 Chirality : 0.037 0.138 4920 Planarity : 0.003 0.034 6192 Dihedral : 4.442 22.190 4536 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 5.20 % Favored : 94.14 % 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: 4.07 (0.12), residues: 4032 helix: 3.15 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.52 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 63 TYR 0.022 0.002 TYR Y 39 PHE 0.017 0.002 PHE A 81 TRP 0.008 0.002 TRP I 93 HIS 0.004 0.001 HIS 2 118 Details of bonding type rmsd covalent geometry : bond 0.00307 (34776) covalent geometry : angle 0.58496 (46848) hydrogen bonds : bond 0.05615 ( 2706) hydrogen bonds : angle 3.77482 ( 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 562 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 538 time to evaluate : 1.485 Fit side-chains REVERT: 2 63 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7408 (ttm-80) REVERT: 6 63 ARG cc_start: 0.7829 (ttp-170) cc_final: 0.7411 (ttm-80) REVERT: F 63 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7448 (ttm-80) REVERT: H 63 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7420 (ttm-80) REVERT: O 63 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7416 (ttm-80) REVERT: P 63 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7402 (ttm-80) REVERT: S 63 ARG cc_start: 0.7828 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: U 63 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7448 (ttm-80) REVERT: W 63 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7408 (ttm-80) outliers start: 24 outliers final: 24 residues processed: 538 average time/residue: 1.0432 time to fit residues: 636.6410 Evaluate side-chains 532 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 508 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain r residue 14 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 201 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 309 optimal weight: 0.6980 chunk 253 optimal weight: 9.9990 chunk 321 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 294 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 1 139 ASN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN U 139 ASN W 86 GLN W 139 ASN X 86 GLN X 139 ASN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.153866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.146886 restraints weight = 18247.885| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 0.27 r_work: 0.3381 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.3018 rms_B_bonded: 2.99 restraints_weight: 0.1250 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1280 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= 0.130 Angle : 0.532 5.062 46848 Z= 0.295 Chirality : 0.036 0.138 4920 Planarity : 0.003 0.030 6192 Dihedral : 4.342 21.987 4536 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 5.50 % Favored : 93.85 % 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: 4.59 (0.13), residues: 4032 helix: 3.52 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.69 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 63 TYR 0.019 0.002 TYR A 39 PHE 0.012 0.002 PHE U 132 TRP 0.009 0.002 TRP 2 93 HIS 0.003 0.001 HIS 2 118 Details of bonding type rmsd covalent geometry : bond 0.00251 (34776) covalent geometry : angle 0.53177 (46848) hydrogen bonds : bond 0.05107 ( 2706) hydrogen bonds : angle 3.62447 ( 8118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20470.80 seconds wall clock time: 347 minutes 32.94 seconds (20852.94 seconds total)