Starting phenix.real_space_refine on Sun Jun 29 08:17:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpu_16786/06_2025/8cpu_16786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpu_16786/06_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_16786/06_2025/8cpu_16786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpu_16786/06_2025/8cpu_16786.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpu_16786/06_2025/8cpu_16786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpu_16786/06_2025/8cpu_16786.cif" } resolution = 1.76 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 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.21, per 1000 atoms: 0.56 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: 8.51 Conformation dependent library (CDL) restraints added in 3.7 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: 2.45 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 77 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 163 through 174 Processing helix chain '2' and resid 13 through 42 Processing helix chain '2' and resid 48 through 77 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 163 through 174 Processing helix chain '4' and resid 13 through 42 Processing helix chain '4' and resid 48 through 77 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 163 through 174 Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 48 through 76 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 163 through 174 Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 77 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 Processing helix chain 'a' and resid 13 through 42 Processing helix chain 'a' and resid 48 through 76 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 163 through 174 Processing helix chain 'e' and resid 13 through 42 Processing helix chain 'e' and resid 48 through 77 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 163 through 174 Processing helix chain 'r' and resid 13 through 42 Processing helix chain 'r' and resid 48 through 77 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 163 through 174 2706 hydrogen bonds defined for protein. 8118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.20 Time building geometry restraints manager: 10.03 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: 0.05 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 70.390 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.250 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.870 ------------------------------------------------------------------------------- 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 (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: 2.29 (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 TRP 0.009 0.002 TRP F 93 HIS 0.008 0.002 HIS P 128 PHE 0.023 0.003 PHE A 41 TYR 0.085 0.007 TYR H 32 ARG 0.016 0.003 ARG F 76 Details of bonding type rmsd hydrogen bonds : bond 0.06845 ( 2706) hydrogen bonds : angle 4.38333 ( 8118) covalent geometry : bond 0.00415 (34776) covalent geometry : angle 0.70740 (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 610 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 3.886 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 2.0722 time to fit residues: 1452.8528 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 : 4.093 ------------------------------------------------------------------------------- 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: 4.9990 chunk 309 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 319 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.151751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.144800 restraints weight = 18357.899| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 0.27 r_work: 0.3348 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.2984 rms_B_bonded: 3.01 restraints_weight: 0.1250 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34776 Z= 0.154 Angle : 0.574 5.319 46848 Z= 0.321 Chirality : 0.038 0.152 4920 Planarity : 0.004 0.021 6192 Dihedral : 4.451 21.283 4536 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.65 % Allowed : 2.48 % Favored : 96.87 % 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: 4.35 (0.13), residues: 4032 helix: 3.28 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.88 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 93 HIS 0.004 0.001 HIS U 128 PHE 0.015 0.002 PHE X 41 TYR 0.045 0.004 TYR S 32 ARG 0.005 0.001 ARG 6 63 Details of bonding type rmsd hydrogen bonds : bond 0.05576 ( 2706) hydrogen bonds : angle 3.80782 ( 8118) covalent geometry : bond 0.00303 (34776) covalent geometry : angle 0.57419 (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 605 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 581 time to evaluate : 4.397 Fit side-chains REVERT: F 63 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7388 (ttt90) REVERT: H 63 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7400 (ttt90) REVERT: S 63 ARG cc_start: 0.7821 (ttp-170) cc_final: 0.7385 (ttm-80) REVERT: U 63 ARG cc_start: 0.7802 (ttp-170) cc_final: 0.7404 (ttm-80) REVERT: W 63 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7385 (ttt90) REVERT: Y 63 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7391 (ttt90) outliers start: 24 outliers final: 0 residues processed: 581 average time/residue: 2.3883 time to fit residues: 1571.2890 Evaluate side-chains 544 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 342 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 316 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.150253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.143435 restraints weight = 18262.026| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.27 r_work: 0.3333 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.2965 rms_B_bonded: 2.95 restraints_weight: 0.1250 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1032 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= 0.200 Angle : 0.666 6.239 46848 Z= 0.368 Chirality : 0.040 0.145 4920 Planarity : 0.004 0.039 6192 Dihedral : 4.511 21.697 4536 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.65 % Allowed : 3.57 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.12), residues: 4032 helix: 3.05 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.55 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP e 93 HIS 0.006 0.002 HIS X 118 PHE 0.020 0.003 PHE Q 81 TYR 0.032 0.004 TYR A 32 ARG 0.007 0.001 ARG W 63 Details of bonding type rmsd hydrogen bonds : bond 0.06259 ( 2706) hydrogen bonds : angle 3.95091 ( 8118) covalent geometry : bond 0.00415 (34776) covalent geometry : angle 0.66610 (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 577 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 553 time to evaluate : 4.111 Fit side-chains REVERT: H 63 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7432 (ttm-80) REVERT: P 63 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7416 (ttm-80) REVERT: S 63 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7398 (ttm-80) REVERT: U 63 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7417 (ttm-80) outliers start: 24 outliers final: 20 residues processed: 553 average time/residue: 2.3826 time to fit residues: 1490.1758 Evaluate side-chains 559 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 539 time to evaluate : 4.491 ------------------------------------------------------------------------------- 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 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 298 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 343 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.150977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.143920 restraints weight = 18144.291| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 0.27 r_work: 0.3340 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2972 rms_B_bonded: 2.96 restraints_weight: 0.1250 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 34776 Z= 0.176 Angle : 0.613 6.096 46848 Z= 0.340 Chirality : 0.038 0.143 4920 Planarity : 0.004 0.046 6192 Dihedral : 4.434 21.896 4536 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.68 % Allowed : 4.14 % Favored : 95.18 % 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: 4.04 (0.12), residues: 4032 helix: 3.12 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.59 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 93 HIS 0.005 0.001 HIS X 118 PHE 0.018 0.003 PHE K 81 TYR 0.023 0.003 TYR r 39 ARG 0.007 0.001 ARG O 63 Details of bonding type rmsd hydrogen bonds : bond 0.05902 ( 2706) hydrogen bonds : angle 3.85207 ( 8118) covalent geometry : bond 0.00359 (34776) covalent geometry : angle 0.61257 (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 585 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 560 time to evaluate : 4.121 Fit side-chains REVERT: 6 63 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7426 (ttm-80) REVERT: F 63 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7411 (ttm-80) REVERT: H 63 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: O 63 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7461 (ttm-80) REVERT: P 63 ARG cc_start: 0.7841 (ttp-170) cc_final: 0.7407 (ttm-80) REVERT: S 63 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7431 (ttm-80) REVERT: U 63 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7435 (ttm-80) REVERT: W 63 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7407 (ttm-80) REVERT: X 63 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7450 (ttm-80) outliers start: 25 outliers final: 24 residues processed: 561 average time/residue: 2.4076 time to fit residues: 1526.0144 Evaluate side-chains 559 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 535 time to evaluate : 4.019 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 6.9990 chunk 392 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 354 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 340 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.150136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.143077 restraints weight = 18125.101| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 0.28 r_work: 0.3329 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.2962 rms_B_bonded: 2.95 restraints_weight: 0.1250 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34776 Z= 0.213 Angle : 0.691 6.671 46848 Z= 0.380 Chirality : 0.041 0.144 4920 Planarity : 0.004 0.044 6192 Dihedral : 4.509 21.785 4536 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 4.00 % Favored : 95.34 % 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: 3.59 (0.12), residues: 4032 helix: 2.81 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.40 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP 2 93 HIS 0.006 0.002 HIS X 118 PHE 0.020 0.003 PHE W 81 TYR 0.028 0.004 TYR S 39 ARG 0.010 0.001 ARG 2 63 Details of bonding type rmsd hydrogen bonds : bond 0.06386 ( 2706) hydrogen bonds : angle 3.97165 ( 8118) covalent geometry : bond 0.00444 (34776) covalent geometry : angle 0.69060 (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 568 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 544 time to evaluate : 4.206 Fit side-chains REVERT: F 63 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7405 (ttm-80) REVERT: H 63 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7419 (ttm-80) REVERT: O 63 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7430 (ttm-80) REVERT: P 63 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7411 (ttm-80) REVERT: S 63 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7435 (ttm-80) REVERT: U 63 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7431 (ttm-80) REVERT: W 63 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7410 (ttm-80) REVERT: X 63 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7410 (ttm-80) outliers start: 24 outliers final: 24 residues processed: 544 average time/residue: 2.4244 time to fit residues: 1501.1587 Evaluate side-chains 558 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 534 time to evaluate : 4.474 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 316 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 401 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 403 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 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 P 139 ASN Q 60 HIS 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 = 0.3586 r_free = 0.3586 target = 0.155430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.148465 restraints weight = 18267.429| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 0.27 r_work: 0.3401 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.3042 rms_B_bonded: 3.00 restraints_weight: 0.1250 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 34776 Z= 0.114 Angle : 0.488 5.150 46848 Z= 0.272 Chirality : 0.035 0.138 4920 Planarity : 0.003 0.027 6192 Dihedral : 4.247 21.674 4536 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 3.65 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.93 (0.13), residues: 4032 helix: 3.77 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.75 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 93 HIS 0.003 0.001 HIS P 128 PHE 0.012 0.002 PHE a 132 TYR 0.017 0.002 TYR U 39 ARG 0.004 0.000 ARG 2 63 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 2706) hydrogen bonds : angle 3.50687 ( 8118) covalent geometry : bond 0.00211 (34776) covalent geometry : angle 0.48812 (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 638 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 614 time to evaluate : 3.900 Fit side-chains REVERT: 6 63 ARG cc_start: 0.7828 (ttp-170) cc_final: 0.7405 (ttt90) REVERT: F 63 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7447 (ttm-80) REVERT: H 63 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7431 (ttm-80) REVERT: O 63 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7396 (ttt90) REVERT: P 63 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7360 (ttt90) REVERT: S 63 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7411 (ttm-80) REVERT: U 63 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7424 (ttm-80) REVERT: W 63 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: X 63 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7383 (ttt90) REVERT: Y 63 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7394 (ttt90) outliers start: 24 outliers final: 0 residues processed: 614 average time/residue: 2.4225 time to fit residues: 1699.3543 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 : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 307 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 282 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 354 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 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 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 G 86 GLN G 139 ASN H 86 GLN H 139 ASN I 60 HIS 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 P 139 ASN ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN Q 109 ASN Q 139 ASN S 86 GLN S 109 ASN S 139 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 Y 139 ASN 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: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.155313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.148219 restraints weight = 18271.188| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 0.27 r_work: 0.3396 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.3034 rms_B_bonded: 2.98 restraints_weight: 0.1250 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 34776 Z= 0.119 Angle : 0.500 4.841 46848 Z= 0.279 Chirality : 0.035 0.132 4920 Planarity : 0.003 0.027 6192 Dihedral : 4.240 22.311 4536 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: 5.01 (0.13), residues: 4032 helix: 3.82 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.77 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 93 HIS 0.003 0.001 HIS B 128 PHE 0.011 0.002 PHE U 132 TYR 0.017 0.002 TYR W 39 ARG 0.004 0.000 ARG Y 63 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 2706) hydrogen bonds : angle 3.52657 ( 8118) covalent geometry : bond 0.00224 (34776) covalent geometry : angle 0.49964 (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 543 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 5.000 Fit side-chains REVERT: F 63 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7395 (ttt90) REVERT: H 63 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7392 (ttt90) REVERT: O 63 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: P 63 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7382 (ttt90) REVERT: S 63 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7368 (ttt90) REVERT: U 63 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7418 (ttm-80) REVERT: W 63 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7390 (ttt90) REVERT: X 63 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7401 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 2.1625 time to fit residues: 1342.9584 Evaluate side-chains 534 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 347 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 346 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 400 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 291 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 2 139 ASN 4 86 GLN 4 112 GLN 4 139 ASN 6 86 GLN 6 109 ASN 6 139 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 H 139 ASN I 60 HIS 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 P 139 ASN Q 60 HIS Q 86 GLN Q 109 ASN Q 139 ASN S 86 GLN S 109 ASN S 139 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 Y 139 ASN 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: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.154449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.147351 restraints weight = 18110.476| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 0.27 r_work: 0.3386 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.3020 rms_B_bonded: 3.00 restraints_weight: 0.1250 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 34776 Z= 0.128 Angle : 0.521 5.003 46848 Z= 0.290 Chirality : 0.035 0.129 4920 Planarity : 0.003 0.026 6192 Dihedral : 4.282 22.464 4536 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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: 4.84 (0.13), residues: 4032 helix: 3.69 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.78 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.003 0.001 HIS X 118 PHE 0.012 0.002 PHE U 81 TYR 0.018 0.002 TYR 1 39 ARG 0.005 0.000 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 2706) hydrogen bonds : angle 3.57366 ( 8118) covalent geometry : bond 0.00248 (34776) covalent geometry : angle 0.52138 (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 550 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 4.540 Fit side-chains REVERT: F 63 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7388 (ttt90) REVERT: H 63 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7375 (ttt90) REVERT: O 63 ARG cc_start: 0.7807 (ttp-170) cc_final: 0.7416 (ttm-80) REVERT: P 63 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7369 (ttt90) REVERT: S 63 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7362 (ttt90) REVERT: U 63 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7390 (ttt90) REVERT: W 63 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7389 (ttt90) REVERT: X 63 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7406 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 550 average time/residue: 2.1688 time to fit residues: 1363.6593 Evaluate side-chains 527 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 249 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 397 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 2 139 ASN 4 86 GLN 4 112 GLN 4 139 ASN 6 86 GLN 6 109 ASN 6 139 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 H 139 ASN I 60 HIS 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 P 139 ASN Q 60 HIS Q 86 GLN Q 109 ASN Q 139 ASN S 86 GLN S 109 ASN S 139 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 Y 139 ASN 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: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.155358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.148290 restraints weight = 18239.533| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 0.27 r_work: 0.3399 rms_B_bonded: 0.52 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.3038 rms_B_bonded: 2.96 restraints_weight: 0.1250 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 34776 Z= 0.121 Angle : 0.506 4.837 46848 Z= 0.283 Chirality : 0.035 0.130 4920 Planarity : 0.003 0.025 6192 Dihedral : 4.241 22.192 4536 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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: 4.95 (0.13), residues: 4032 helix: 3.77 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.78 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP 4 93 HIS 0.003 0.001 HIS F 128 PHE 0.011 0.002 PHE U 132 TYR 0.016 0.002 TYR A 39 ARG 0.005 0.000 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 2706) hydrogen bonds : angle 3.52205 ( 8118) covalent geometry : bond 0.00233 (34776) covalent geometry : angle 0.50641 (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 546 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 546 time to evaluate : 4.405 Fit side-chains REVERT: F 63 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7386 (ttt90) REVERT: H 63 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7424 (ttt90) REVERT: O 63 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7469 (ttm-80) REVERT: P 63 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7365 (ttt90) REVERT: S 63 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7416 (ttt90) REVERT: U 63 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.7418 (ttm-80) REVERT: W 63 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7380 (ttt90) REVERT: X 63 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7395 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 546 average time/residue: 2.1751 time to fit residues: 1357.1197 Evaluate side-chains 531 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 4.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 241 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 339 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 2 139 ASN 4 86 GLN 4 112 GLN 4 139 ASN 6 86 GLN 6 109 ASN 6 139 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 H 139 ASN I 60 HIS 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 P 139 ASN Q 60 HIS Q 86 GLN Q 109 ASN Q 139 ASN S 86 GLN S 109 ASN S 139 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 Y 139 ASN 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: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.152168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.145044 restraints weight = 18083.230| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 0.27 r_work: 0.3356 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.2987 rms_B_bonded: 2.99 restraints_weight: 0.1250 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1316 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= 0.172 Angle : 0.614 5.652 46848 Z= 0.340 Chirality : 0.038 0.127 4920 Planarity : 0.004 0.039 6192 Dihedral : 4.420 23.140 4536 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 5.77 % 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: 4.26 (0.12), residues: 4032 helix: 3.27 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.66 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 93 HIS 0.005 0.001 HIS X 118 PHE 0.018 0.002 PHE 6 81 TYR 0.024 0.003 TYR 1 39 ARG 0.010 0.001 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.05801 ( 2706) hydrogen bonds : angle 3.78401 ( 8118) covalent geometry : bond 0.00355 (34776) covalent geometry : angle 0.61414 (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 512 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 4.378 Fit side-chains REVERT: O 63 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: P 63 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7375 (ttm-80) REVERT: S 63 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7397 (ttm-80) REVERT: U 63 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7364 (ttm-80) REVERT: W 63 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7398 (ttm-80) REVERT: X 63 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7399 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 2.2767 time to fit residues: 1326.1220 Evaluate side-chains 496 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 167 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 195 optimal weight: 0.3980 chunk 374 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 331 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 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 60 HIS I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 60 HIS Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN S 139 ASN U 86 GLN W 86 GLN X 86 GLN X 139 ASN Y 86 GLN Y 112 GLN Y 139 ASN a 86 GLN e 86 GLN e 112 GLN e 139 ASN r 86 GLN r 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.154943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.147874 restraints weight = 18206.733| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 0.27 r_work: 0.3379 rms_B_bonded: 0.59 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.3017 rms_B_bonded: 3.30 restraints_weight: 0.1250 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 34776 Z= 0.126 Angle : 0.523 5.123 46848 Z= 0.292 Chirality : 0.035 0.134 4920 Planarity : 0.003 0.026 6192 Dihedral : 4.278 22.582 4536 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.75 (0.13), residues: 4032 helix: 3.64 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.72 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 93 HIS 0.003 0.001 HIS U 118 PHE 0.011 0.002 PHE 2 81 TYR 0.017 0.002 TYR r 39 ARG 0.006 0.000 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 2706) hydrogen bonds : angle 3.57345 ( 8118) covalent geometry : bond 0.00243 (34776) covalent geometry : angle 0.52282 (46848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47603.29 seconds wall clock time: 825 minutes 32.51 seconds (49532.51 seconds total)