Starting phenix.real_space_refine on Sun Jun 29 12:02:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cps_16784/06_2025/8cps_16784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cps_16784/06_2025/8cps_16784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cps_16784/06_2025/8cps_16784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cps_16784/06_2025/8cps_16784.map" model { file = "/net/cci-nas-00/data/ceres_data/8cps_16784/06_2025/8cps_16784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cps_16784/06_2025/8cps_16784.cif" } resolution = 1.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 8540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 36034 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "2" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "4" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "6" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "M" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "O" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "P" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "Q" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "S" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "W" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "X" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Y" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "a" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "e" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "r" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Time building chain proxies: 22.70, per 1000 atoms: 0.63 Number of scatterers: 36034 At special positions: 0 Unit cell: (131.856, 131.856, 131.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 Mg 14 11.99 Na 24 11.00 O 8540 8.00 N 5976 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 4.2 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 77 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 163 through 174 Processing helix chain '2' and resid 13 through 42 Processing helix chain '2' and resid 48 through 77 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 163 through 174 Processing helix chain '4' and resid 13 through 42 Processing helix chain '4' and resid 48 through 77 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 163 through 174 Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 48 through 76 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 163 through 174 Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 77 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 Processing helix chain 'a' and resid 13 through 42 Processing helix chain 'a' and resid 48 through 76 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 163 through 174 Processing helix chain 'e' and resid 13 through 42 Processing helix chain 'e' and resid 48 through 77 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 163 through 174 Processing helix chain 'r' and resid 13 through 42 Processing helix chain 'r' and resid 48 through 77 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 163 through 174 2706 hydrogen bonds defined for protein. 8118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.40 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11664 1.34 - 1.46: 5786 1.46 - 1.58: 17062 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX O 90 " pdb=" SG CSX O 90 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CSX e 90 " pdb=" SG CSX e 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CB CSX 6 90 " pdb=" SG CSX 6 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 44796 1.35 - 2.70: 1626 2.70 - 4.04: 281 4.04 - 5.39: 121 5.39 - 6.74: 24 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR E 39 " pdb=" CB TYR E 39 " pdb=" CG TYR E 39 " ideal model delta sigma weight residual 113.90 108.70 5.20 1.80e+00 3.09e-01 8.35e+00 angle pdb=" CA TYR I 39 " pdb=" CB TYR I 39 " pdb=" CG TYR I 39 " ideal model delta sigma weight residual 113.90 108.72 5.18 1.80e+00 3.09e-01 8.28e+00 angle pdb=" CA TYR 1 39 " pdb=" CB TYR 1 39 " pdb=" CG TYR 1 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" CA TYR Q 39 " pdb=" CB TYR Q 39 " pdb=" CG TYR Q 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" CA TYR M 39 " pdb=" CB TYR M 39 " pdb=" CG TYR M 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 19184 17.67 - 35.34: 1270 35.34 - 53.02: 323 53.02 - 70.69: 86 70.69 - 88.36: 137 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA VAL X 46 " pdb=" C VAL X 46 " pdb=" N ALA X 47 " pdb=" CA ALA X 47 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA VAL Q 46 " pdb=" C VAL Q 46 " pdb=" N ALA Q 47 " pdb=" CA ALA Q 47 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3644 0.043 - 0.085: 923 0.085 - 0.128: 252 0.128 - 0.171: 59 0.171 - 0.213: 42 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR K 137 " pdb=" N TYR K 137 " pdb=" C TYR K 137 " pdb=" CB TYR K 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA TYR O 137 " pdb=" N TYR O 137 " pdb=" C TYR O 137 " pdb=" CB TYR O 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA TYR P 137 " pdb=" N TYR P 137 " pdb=" C TYR P 137 " pdb=" CB TYR P 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 137 " -0.022 2.00e-02 2.50e+03 1.55e-02 4.81e+00 pdb=" CG TYR H 137 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR H 137 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 137 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR H 137 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR H 137 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Y 137 " 0.022 2.00e-02 2.50e+03 1.55e-02 4.80e+00 pdb=" CG TYR Y 137 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR Y 137 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR Y 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR Y 137 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR Y 137 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Y 137 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR Y 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 137 " -0.022 2.00e-02 2.50e+03 1.55e-02 4.78e+00 pdb=" CG TYR B 137 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 137 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 137 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 137 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 137 " -0.018 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1707 2.67 - 3.23: 37105 3.23 - 3.79: 69892 3.79 - 4.34: 94158 4.34 - 4.90: 146205 Nonbonded interactions: 349067 Sorted by model distance: nonbonded pdb=" OD1 ASP 1 123 " pdb=" O HOH 1 301 " model vdw 2.116 3.040 nonbonded pdb=" OD1 ASP e 123 " pdb=" O HOH e 601 " model vdw 2.116 3.040 nonbonded pdb=" OD1 ASP B 123 " pdb=" O HOH B 601 " model vdw 2.117 3.040 nonbonded pdb=" OD1 ASP A 123 " pdb=" O HOH A 601 " model vdw 2.117 3.040 nonbonded pdb=" OD1 ASP O 123 " pdb=" O HOH O 601 " model vdw 2.117 3.040 ... (remaining 349062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain '1' and resid 4 through 176) selection = (chain '2' and resid 4 through 176) selection = (chain '4' and resid 4 through 176) selection = (chain '6' and resid 4 through 176) selection = (chain 'A' and resid 4 through 176) selection = (chain 'B' and resid 4 through 176) selection = (chain 'E' and resid 4 through 176) selection = (chain 'F' and resid 4 through 176) selection = (chain 'G' and resid 4 through 176) selection = (chain 'H' and resid 4 through 176) selection = (chain 'I' and resid 4 through 176) selection = (chain 'K' and resid 4 through 176) selection = (chain 'M' and resid 4 through 176) selection = (chain 'O' and resid 4 through 176) selection = (chain 'P' and resid 4 through 176) selection = (chain 'Q' and resid 4 through 176) selection = (chain 'S' and resid 4 through 176) selection = (chain 'U' and resid 4 through 176) selection = (chain 'W' and resid 4 through 176) selection = (chain 'X' and resid 4 through 176) selection = (chain 'Y' and resid 4 through 176) selection = (chain 'a' and resid 4 through 176) selection = (chain 'e' and resid 4 through 176) selection = (chain 'r' and resid 4 through 176) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.060 Extract box with map and model: 1.600 Check model and map are aligned: 0.280 Set scattering table: 0.370 Process input model: 78.750 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34776 Z= 0.178 Angle : 0.660 6.742 46848 Z= 0.373 Chirality : 0.045 0.213 4920 Planarity : 0.006 0.055 6192 Dihedral : 15.421 88.361 13032 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.13), residues: 4032 helix: 1.70 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.94 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 93 HIS 0.009 0.002 HIS F 128 PHE 0.021 0.003 PHE I 41 TYR 0.029 0.004 TYR B 137 ARG 0.015 0.003 ARG r 76 Details of bonding type rmsd hydrogen bonds : bond 0.06325 ( 2706) hydrogen bonds : angle 4.26205 ( 8118) covalent geometry : bond 0.00339 (34776) covalent geometry : angle 0.65962 (46848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 738 time to evaluate : 3.936 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 738 average time/residue: 2.7611 time to fit residues: 2343.9628 Evaluate side-chains 684 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 9.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 0.2980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 105 HIS 1 139 ASN 2 60 HIS 2 83 GLN 2 105 HIS 2 139 ASN 4 60 HIS 4 83 GLN 4 105 HIS 4 139 ASN 6 60 HIS 6 83 GLN 6 105 HIS 6 139 ASN A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS E 139 ASN F 83 GLN F 105 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS H 139 ASN I 83 GLN I 105 HIS I 139 ASN K 60 HIS K 83 GLN K 105 HIS K 139 ASN M 83 GLN M 105 HIS M 139 ASN M 141 GLN O 83 GLN O 105 HIS O 139 ASN P 83 GLN P 105 HIS P 139 ASN Q 83 GLN Q 105 HIS Q 141 GLN S 83 GLN S 105 HIS U 60 HIS U 83 GLN U 105 HIS U 139 ASN W 83 GLN W 105 HIS X 83 GLN X 105 HIS X 139 ASN Y 83 GLN Y 105 HIS Y 139 ASN a 83 GLN a 105 HIS e 83 GLN e 105 HIS e 139 ASN r 83 GLN r 105 HIS r 139 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.155669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.148901 restraints weight = 20169.849| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 0.32 r_work: 0.3254 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 1.20 restraints_weight: 0.2500 r_work: 0.2897 rms_B_bonded: 3.46 restraints_weight: 0.1250 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0842 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 : 0.672 6.510 46848 Z= 0.365 Chirality : 0.043 0.156 4920 Planarity : 0.004 0.059 6192 Dihedral : 5.195 32.735 4536 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.33 (0.13), residues: 4032 helix: 3.19 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.28 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP U 93 HIS 0.006 0.001 HIS X 128 PHE 0.025 0.004 PHE 4 41 TYR 0.027 0.004 TYR G 39 ARG 0.006 0.001 ARG 2 63 Details of bonding type rmsd hydrogen bonds : bond 0.05798 ( 2706) hydrogen bonds : angle 3.91492 ( 8118) covalent geometry : bond 0.00373 (34776) covalent geometry : angle 0.67200 (46848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 705 time to evaluate : 3.845 Fit side-chains REVERT: Q 123 ASP cc_start: 0.7091 (m-30) cc_final: 0.6887 (m-30) outliers start: 1 outliers final: 1 residues processed: 705 average time/residue: 2.0392 time to fit residues: 1654.4972 Evaluate side-chains 679 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 119 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 332 optimal weight: 5.9990 chunk 315 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 105 HIS 1 139 ASN 2 83 GLN 2 105 HIS 2 139 ASN 4 60 HIS 4 83 GLN 4 105 HIS 4 139 ASN 6 60 HIS 6 83 GLN 6 105 HIS 6 139 ASN A 83 GLN A 105 HIS B 83 GLN B 105 HIS E 83 GLN E 105 HIS E 139 ASN F 83 GLN F 105 HIS G 60 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS H 139 ASN I 83 GLN I 105 HIS I 139 ASN K 60 HIS K 83 GLN K 105 HIS K 139 ASN M 83 GLN M 105 HIS M 139 ASN O 83 GLN O 105 HIS O 139 ASN P 83 GLN P 105 HIS P 139 ASN Q 83 GLN Q 105 HIS S 83 GLN S 105 HIS U 60 HIS U 83 GLN U 105 HIS U 139 ASN W 83 GLN W 105 HIS X 83 GLN X 105 HIS X 139 ASN Y 83 GLN Y 105 HIS Y 139 ASN a 83 GLN a 105 HIS e 83 GLN e 105 HIS e 139 ASN r 83 GLN r 105 HIS r 139 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.155092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.148255 restraints weight = 20184.468| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.31 r_work: 0.3246 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2886 rms_B_bonded: 3.52 restraints_weight: 0.1250 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 34776 Z= 0.226 Angle : 0.722 7.042 46848 Z= 0.395 Chirality : 0.044 0.151 4920 Planarity : 0.004 0.053 6192 Dihedral : 5.312 36.310 4536 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 5.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.13), residues: 4032 helix: 3.11 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.58 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP P 93 HIS 0.006 0.001 HIS I 128 PHE 0.027 0.004 PHE A 41 TYR 0.029 0.004 TYR 4 39 ARG 0.006 0.001 ARG K 63 Details of bonding type rmsd hydrogen bonds : bond 0.06218 ( 2706) hydrogen bonds : angle 4.03904 ( 8118) covalent geometry : bond 0.00459 (34776) covalent geometry : angle 0.72180 (46848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 702 time to evaluate : 4.301 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 702 average time/residue: 2.2287 time to fit residues: 1798.5407 Evaluate side-chains 678 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 677 time to evaluate : 4.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 99 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 322 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 242 optimal weight: 9.9990 chunk 405 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 2 83 GLN 4 83 GLN 4 136 HIS 6 83 GLN A 83 GLN B 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 60 HIS I 83 GLN K 83 GLN M 83 GLN O 83 GLN O 136 HIS P 83 GLN Q 60 HIS Q 83 GLN S 83 GLN U 83 GLN W 83 GLN X 83 GLN Y 83 GLN a 83 GLN e 83 GLN e 136 HIS r 83 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.156692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.149844 restraints weight = 20224.130| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 0.31 r_work: 0.3267 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2908 rms_B_bonded: 3.50 restraints_weight: 0.1250 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34776 Z= 0.173 Angle : 0.639 6.861 46848 Z= 0.348 Chirality : 0.041 0.141 4920 Planarity : 0.004 0.048 6192 Dihedral : 5.067 31.003 4536 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.11 % Allowed : 5.94 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.70 (0.13), residues: 4032 helix: 3.41 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.64 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP 2 93 HIS 0.005 0.001 HIS 1 128 PHE 0.022 0.003 PHE E 41 TYR 0.026 0.003 TYR r 39 ARG 0.005 0.001 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.05613 ( 2706) hydrogen bonds : angle 3.84776 ( 8118) covalent geometry : bond 0.00342 (34776) covalent geometry : angle 0.63863 (46848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 719 time to evaluate : 6.384 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 719 average time/residue: 2.9454 time to fit residues: 2445.8691 Evaluate side-chains 675 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 674 time to evaluate : 13.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 201 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 407 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 136 HIS 2 83 GLN 4 83 GLN 6 83 GLN A 83 GLN A 136 HIS B 83 GLN B 136 HIS E 60 HIS E 83 GLN E 136 HIS F 83 GLN F 136 HIS G 83 GLN H 60 HIS H 83 GLN I 60 HIS I 83 GLN I 136 HIS K 83 GLN K 136 HIS M 60 HIS M 83 GLN O 83 GLN P 83 GLN Q 60 HIS Q 83 GLN S 83 GLN S 136 HIS U 83 GLN U 136 HIS W 60 HIS W 83 GLN X 83 GLN X 136 HIS Y 83 GLN a 83 GLN e 83 GLN r 83 GLN r 136 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.156405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.149539 restraints weight = 20193.800| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 0.32 r_work: 0.3265 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2906 rms_B_bonded: 3.50 restraints_weight: 0.1250 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34776 Z= 0.179 Angle : 0.645 6.785 46848 Z= 0.352 Chirality : 0.041 0.142 4920 Planarity : 0.004 0.049 6192 Dihedral : 5.083 31.105 4536 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.70 (0.13), residues: 4032 helix: 3.40 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.66 (0.30), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP Q 93 HIS 0.005 0.001 HIS M 60 PHE 0.022 0.003 PHE Q 41 TYR 0.026 0.003 TYR r 39 ARG 0.005 0.001 ARG K 63 Details of bonding type rmsd hydrogen bonds : bond 0.05680 ( 2706) hydrogen bonds : angle 3.86232 ( 8118) covalent geometry : bond 0.00356 (34776) covalent geometry : angle 0.64455 (46848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 685 time to evaluate : 4.177 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 685 average time/residue: 2.0721 time to fit residues: 1629.0279 Evaluate side-chains 689 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 688 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 267 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 402 optimal weight: 5.9990 chunk 369 optimal weight: 2.9990 chunk 271 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 2 83 GLN 4 60 HIS 4 83 GLN 6 60 HIS 6 83 GLN A 83 GLN A 86 GLN B 83 GLN B 86 GLN E 83 GLN F 83 GLN F 86 GLN G 83 GLN G 86 GLN H 83 GLN I 83 GLN I 86 GLN K 60 HIS K 83 GLN K 86 GLN M 83 GLN M 86 GLN O 83 GLN P 83 GLN P 86 GLN Q 83 GLN Q 86 GLN S 83 GLN S 86 GLN U 60 HIS U 83 GLN W 83 GLN X 83 GLN Y 83 GLN Y 86 GLN a 83 GLN e 83 GLN e 86 GLN r 83 GLN r 86 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.159406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.152691 restraints weight = 20055.549| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 0.31 r_work: 0.3323 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2968 rms_B_bonded: 3.15 restraints_weight: 0.1250 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 34776 Z= 0.127 Angle : 0.551 5.867 46848 Z= 0.298 Chirality : 0.037 0.134 4920 Planarity : 0.003 0.045 6192 Dihedral : 4.649 22.955 4536 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.17 (0.13), residues: 4032 helix: 3.79 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.49 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Y 93 HIS 0.004 0.001 HIS K 60 PHE 0.015 0.002 PHE 2 41 TYR 0.021 0.002 TYR F 39 ARG 0.002 0.001 ARG 6 22 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 2706) hydrogen bonds : angle 3.60509 ( 8118) covalent geometry : bond 0.00243 (34776) covalent geometry : angle 0.55056 (46848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 707 time to evaluate : 3.990 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 707 average time/residue: 2.0247 time to fit residues: 1645.9743 Evaluate side-chains 686 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 686 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 228 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 292 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 204 optimal weight: 0.0470 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 60 HIS 2 83 GLN 2 86 GLN 2 105 HIS 4 60 HIS 4 83 GLN 4 86 GLN 4 105 HIS 6 60 HIS 6 83 GLN 6 86 GLN 6 105 HIS 6 136 HIS A 83 GLN A 86 GLN A 105 HIS B 83 GLN B 86 GLN B 105 HIS E 60 HIS E 83 GLN E 86 GLN E 105 HIS E 136 HIS F 83 GLN F 86 GLN F 105 HIS G 60 HIS G 83 GLN G 86 GLN G 105 HIS G 136 HIS H 60 HIS H 83 GLN H 86 GLN H 105 HIS I 83 GLN I 86 GLN I 105 HIS K 60 HIS K 83 GLN K 86 GLN K 105 HIS M 60 HIS M 83 GLN M 86 GLN M 105 HIS M 136 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 83 GLN Q 86 GLN Q 105 HIS Q 136 HIS S 83 GLN S 86 GLN S 105 HIS U 60 HIS U 83 GLN U 86 GLN U 105 HIS W 60 HIS W 83 GLN W 86 GLN W 105 HIS W 136 HIS X 83 GLN X 86 GLN X 105 HIS X 136 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS a 136 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS r 136 HIS Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.155676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.148778 restraints weight = 20385.122| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 0.32 r_work: 0.3258 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2900 rms_B_bonded: 3.46 restraints_weight: 0.1250 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34776 Z= 0.215 Angle : 0.698 7.262 46848 Z= 0.382 Chirality : 0.043 0.151 4920 Planarity : 0.004 0.043 6192 Dihedral : 5.096 31.040 4536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.13), residues: 4032 helix: 3.31 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.74 (0.30), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I 93 HIS 0.005 0.001 HIS A 128 PHE 0.025 0.004 PHE a 41 TYR 0.028 0.004 TYR e 39 ARG 0.007 0.001 ARG K 63 Details of bonding type rmsd hydrogen bonds : bond 0.06015 ( 2706) hydrogen bonds : angle 3.96682 ( 8118) covalent geometry : bond 0.00435 (34776) covalent geometry : angle 0.69772 (46848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 4.162 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 2.0632 time to fit residues: 1616.5209 Evaluate side-chains 681 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 391 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 260 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 1 136 HIS 2 83 GLN 2 86 GLN 2 105 HIS 4 83 GLN 4 86 GLN 4 105 HIS 6 60 HIS 6 83 GLN 6 86 GLN 6 105 HIS A 83 GLN A 86 GLN A 105 HIS A 136 HIS B 83 GLN B 86 GLN B 105 HIS B 136 HIS E 60 HIS E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN F 105 HIS F 136 HIS G 83 GLN G 86 GLN G 105 HIS H 60 HIS H 83 GLN H 86 GLN H 105 HIS I 60 HIS I 83 GLN I 86 GLN I 105 HIS I 136 HIS K 60 HIS K 83 GLN K 86 GLN K 105 HIS K 136 HIS M 60 HIS M 83 GLN M 86 GLN M 105 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 60 HIS Q 83 GLN Q 86 GLN Q 105 HIS S 83 GLN S 86 GLN S 105 HIS S 136 HIS U 83 GLN U 86 GLN U 105 HIS U 136 HIS W 60 HIS W 83 GLN W 86 GLN W 105 HIS X 83 GLN X 86 GLN X 105 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.156435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.149577 restraints weight = 20258.882| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 0.32 r_work: 0.3270 rms_B_bonded: 0.61 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 1.20 restraints_weight: 0.2500 r_work: 0.2911 rms_B_bonded: 3.45 restraints_weight: 0.1250 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34776 Z= 0.186 Angle : 0.652 6.779 46848 Z= 0.357 Chirality : 0.041 0.141 4920 Planarity : 0.004 0.048 6192 Dihedral : 4.995 28.427 4536 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.68 (0.13), residues: 4032 helix: 3.38 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.67 (0.30), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 93 HIS 0.004 0.001 HIS 1 128 PHE 0.023 0.004 PHE I 41 TYR 0.027 0.003 TYR e 39 ARG 0.006 0.001 ARG 2 63 Details of bonding type rmsd hydrogen bonds : bond 0.05683 ( 2706) hydrogen bonds : angle 3.87468 ( 8118) covalent geometry : bond 0.00372 (34776) covalent geometry : angle 0.65233 (46848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 4.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 2.0788 time to fit residues: 1640.8803 Evaluate side-chains 672 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 304 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 367 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 173 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 309 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 402 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 60 HIS 2 83 GLN 2 86 GLN 2 105 HIS 4 60 HIS 4 83 GLN 4 86 GLN 4 105 HIS 6 60 HIS 6 83 GLN 6 86 GLN 6 105 HIS A 83 GLN A 86 GLN A 105 HIS B 83 GLN B 86 GLN B 105 HIS E 60 HIS E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN F 105 HIS G 60 HIS G 83 GLN G 86 GLN G 105 HIS H 83 GLN H 86 GLN H 105 HIS I 83 GLN I 86 GLN I 105 HIS K 60 HIS K 83 GLN K 86 GLN K 105 HIS M 83 GLN M 86 GLN M 105 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 83 GLN Q 86 GLN Q 105 HIS S 83 GLN S 86 GLN S 105 HIS U 60 HIS U 83 GLN U 86 GLN U 105 HIS W 60 HIS W 83 GLN W 86 GLN W 105 HIS X 83 GLN X 86 GLN X 105 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.157428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.150680 restraints weight = 20309.979| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 0.33 r_work: 0.3298 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.2938 rms_B_bonded: 3.15 restraints_weight: 0.1250 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34776 Z= 0.160 Angle : 0.614 6.443 46848 Z= 0.335 Chirality : 0.040 0.138 4920 Planarity : 0.004 0.047 6192 Dihedral : 4.861 24.781 4536 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.13), residues: 4032 helix: 3.53 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.59 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 93 HIS 0.004 0.001 HIS 4 60 PHE 0.020 0.003 PHE I 41 TYR 0.025 0.003 TYR X 39 ARG 0.005 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.05354 ( 2706) hydrogen bonds : angle 3.77746 ( 8118) covalent geometry : bond 0.00316 (34776) covalent geometry : angle 0.61442 (46848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 4.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 2.0496 time to fit residues: 1620.8897 Evaluate side-chains 676 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 676 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 131 optimal weight: 0.9990 chunk 331 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 344 optimal weight: 0.7980 chunk 364 optimal weight: 7.9990 chunk 368 optimal weight: 3.9990 chunk 393 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 83 GLN 2 86 GLN 2 105 HIS 4 83 GLN 4 86 GLN 4 105 HIS 6 83 GLN 6 86 GLN 6 105 HIS A 83 GLN A 86 GLN A 105 HIS B 83 GLN B 86 GLN B 105 HIS E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN F 105 HIS G 83 GLN G 86 GLN G 105 HIS H 60 HIS H 83 GLN H 86 GLN H 105 HIS I 83 GLN I 86 GLN I 105 HIS K 83 GLN K 86 GLN K 105 HIS M 60 HIS M 83 GLN M 86 GLN M 105 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 83 GLN Q 86 GLN Q 105 HIS S 83 GLN S 86 GLN S 105 HIS U 83 GLN U 86 GLN U 105 HIS W 83 GLN W 86 GLN W 105 HIS X 83 GLN X 86 GLN X 105 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.158297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.151639 restraints weight = 20094.416| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 0.31 r_work: 0.3312 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2952 rms_B_bonded: 3.16 restraints_weight: 0.1250 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34776 Z= 0.147 Angle : 0.596 6.167 46848 Z= 0.324 Chirality : 0.039 0.136 4920 Planarity : 0.003 0.049 6192 Dihedral : 4.725 22.729 4536 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 6.78 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.94 (0.13), residues: 4032 helix: 3.61 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.53 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 93 HIS 0.004 0.001 HIS I 128 PHE 0.018 0.003 PHE I 41 TYR 0.023 0.003 TYR G 39 ARG 0.008 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 2706) hydrogen bonds : angle 3.72373 ( 8118) covalent geometry : bond 0.00287 (34776) covalent geometry : angle 0.59553 (46848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 684 time to evaluate : 4.355 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 684 average time/residue: 2.0720 time to fit residues: 1627.8472 Evaluate side-chains 682 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 314 optimal weight: 0.9990 chunk 325 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 403 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 60 HIS 2 83 GLN 2 86 GLN 2 105 HIS 4 60 HIS 4 83 GLN 4 86 GLN 4 105 HIS 6 83 GLN 6 86 GLN 6 105 HIS 6 136 HIS A 83 GLN A 86 GLN A 105 HIS B 83 GLN B 86 GLN B 105 HIS E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN F 105 HIS G 60 HIS G 83 GLN G 86 GLN G 105 HIS G 136 HIS H 83 GLN H 86 GLN H 105 HIS I 83 GLN I 86 GLN I 105 HIS K 83 GLN K 86 GLN K 105 HIS M 83 GLN M 86 GLN M 105 HIS M 136 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 83 GLN Q 86 GLN Q 105 HIS Q 136 HIS S 83 GLN S 86 GLN S 105 HIS U 60 HIS U 83 GLN U 86 GLN U 105 HIS W 83 GLN W 86 GLN W 105 HIS W 136 HIS X 83 GLN X 86 GLN X 105 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS a 136 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.157303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.150341 restraints weight = 20142.756| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 0.32 r_work: 0.3281 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 1.20 restraints_weight: 0.2500 r_work: 0.2920 rms_B_bonded: 3.49 restraints_weight: 0.1250 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34776 Z= 0.170 Angle : 0.639 6.794 46848 Z= 0.349 Chirality : 0.041 0.138 4920 Planarity : 0.004 0.051 6192 Dihedral : 4.805 22.680 4536 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.72 (0.13), residues: 4032 helix: 3.42 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.65 (0.30), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 93 HIS 0.004 0.001 HIS E 136 PHE 0.021 0.003 PHE I 41 TYR 0.025 0.003 TYR B 39 ARG 0.008 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 2706) hydrogen bonds : angle 3.84289 ( 8118) covalent geometry : bond 0.00337 (34776) covalent geometry : angle 0.63865 (46848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45072.18 seconds wall clock time: 777 minutes 9.13 seconds (46629.13 seconds total)