Starting phenix.real_space_refine on Tue Aug 26 06:58:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpm_16783/08_2025/8cpm_16783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpm_16783/08_2025/8cpm_16783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cpm_16783/08_2025/8cpm_16783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpm_16783/08_2025/8cpm_16783.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpm_16783/08_2025/8cpm_16783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpm_16783/08_2025/8cpm_16783.cif" } resolution = 1.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 8596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36090 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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "2" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "4" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "6" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "I" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "K" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "M" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "Q" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "W" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "Y" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "a" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "e" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "r" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 6.51, per 1000 atoms: 0.18 Number of scatterers: 36090 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 8596 8.00 N 5976 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 76 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 76 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 76 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 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 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 2688 hydrogen bonds defined for protein. 8064 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: 6.35 Time building geometry restraints manager: 4.06 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: 11626 1.34 - 1.46: 4673 1.46 - 1.57: 18213 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX 4 90 " pdb=" SG CSX 4 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX 6 90 " pdb=" SG CSX 6 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX a 90 " pdb=" SG CSX a 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX e 90 " pdb=" SG CSX e 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX Q 90 " pdb=" SG CSX Q 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 43653 1.43 - 2.86: 2300 2.86 - 4.29: 653 4.29 - 5.72: 187 5.72 - 7.15: 55 Bond angle restraints: 46848 Sorted by residual: angle pdb=" C ARG S 63 " pdb=" CA ARG S 63 " pdb=" CB ARG S 63 " ideal model delta sigma weight residual 110.79 104.61 6.18 1.66e+00 3.63e-01 1.38e+01 angle pdb=" C TYR U 32 " pdb=" CA TYR U 32 " pdb=" CB TYR U 32 " ideal model delta sigma weight residual 110.85 116.36 -5.51 1.70e+00 3.46e-01 1.05e+01 angle pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta sigma weight residual 110.85 116.32 -5.47 1.70e+00 3.46e-01 1.03e+01 angle pdb=" C TYR 6 32 " pdb=" CA TYR 6 32 " pdb=" CB TYR 6 32 " ideal model delta sigma weight residual 110.85 116.32 -5.47 1.70e+00 3.46e-01 1.03e+01 angle pdb=" C TYR S 32 " pdb=" CA TYR S 32 " pdb=" CB TYR S 32 " ideal model delta sigma weight residual 110.85 116.31 -5.46 1.70e+00 3.46e-01 1.03e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 18750 16.54 - 33.08: 1664 33.08 - 49.62: 368 49.62 - 66.16: 102 66.16 - 82.70: 116 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA ASP Y 44 " pdb=" CB ASP Y 44 " pdb=" CG ASP Y 44 " pdb=" OD1 ASP Y 44 " ideal model delta sinusoidal sigma weight residual -30.00 -88.25 58.25 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP I 44 " pdb=" CB ASP I 44 " pdb=" CG ASP I 44 " pdb=" OD1 ASP I 44 " ideal model delta sinusoidal sigma weight residual -30.00 -88.22 58.22 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP 1 44 " pdb=" CB ASP 1 44 " pdb=" CG ASP 1 44 " pdb=" OD1 ASP 1 44 " ideal model delta sinusoidal sigma weight residual -30.00 -88.21 58.21 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3487 0.048 - 0.096: 1092 0.096 - 0.144: 241 0.144 - 0.192: 58 0.192 - 0.240: 42 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR a 39 " pdb=" N TYR a 39 " pdb=" C TYR a 39 " pdb=" CB TYR a 39 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TYR A 137 " pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CB TYR A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA TYR F 137 " pdb=" N TYR F 137 " pdb=" C TYR F 137 " pdb=" CB TYR F 137 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR r 32 " 0.043 2.00e-02 2.50e+03 3.75e-02 2.81e+01 pdb=" CG TYR r 32 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TYR r 32 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR r 32 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR r 32 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR r 32 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR r 32 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR r 32 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 32 " -0.043 2.00e-02 2.50e+03 3.75e-02 2.81e+01 pdb=" CG TYR K 32 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TYR K 32 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR K 32 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR K 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR K 32 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR K 32 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR K 32 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 32 " 0.043 2.00e-02 2.50e+03 3.74e-02 2.80e+01 pdb=" CG TYR 6 32 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 32 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 32 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 32 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 32 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR 6 32 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR 6 32 " 0.003 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 1185 2.51 - 3.11: 29779 3.11 - 3.71: 67484 3.71 - 4.30: 99130 4.30 - 4.90: 155253 Nonbonded interactions: 352831 Sorted by model distance: nonbonded pdb=" O LEU Y 35 " pdb=" O HOH Y 601 " model vdw 1.916 3.040 nonbonded pdb=" O LEU 6 35 " pdb=" O HOH 6 301 " model vdw 1.916 3.040 nonbonded pdb=" O LEU S 35 " pdb=" O HOH S 601 " model vdw 1.917 3.040 nonbonded pdb=" O LEU K 35 " pdb=" O HOH K 601 " model vdw 1.917 3.040 nonbonded pdb=" O LEU G 35 " pdb=" O HOH G 301 " model vdw 1.917 3.040 ... (remaining 352826 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: 0.02 Found NCS groups: ncs_group { reference = (chain '1' and resid 4 through 201) selection = (chain '2' and resid 4 through 201) selection = (chain '4' and resid 4 through 201) selection = (chain '6' and resid 4 through 201) selection = (chain 'A' and resid 4 through 500) selection = (chain 'B' and resid 4 through 500) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 4 through 201) selection = (chain 'H' and resid 4 through 201) selection = chain 'I' selection = chain 'K' selection = (chain 'M' and resid 4 through 201) selection = (chain 'O' and resid 4 through 500) selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.560 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 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 : 0.005 0.075 34776 Z= 0.245 Angle : 0.848 7.146 46848 Z= 0.456 Chirality : 0.054 0.240 4920 Planarity : 0.008 0.067 6192 Dihedral : 15.213 82.695 13032 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.13), residues: 4032 helix: 1.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.00 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG 6 9 TYR 0.092 0.007 TYR r 32 PHE 0.022 0.003 PHE A 41 TRP 0.020 0.004 TRP 1 93 HIS 0.015 0.002 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00525 (34776) covalent geometry : angle 0.84800 (46848) hydrogen bonds : bond 0.06030 ( 2688) hydrogen bonds : angle 4.31313 ( 8064) *********************** 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 615 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.7945 time to fit residues: 563.4055 Evaluate side-chains 562 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 2 60 HIS 2 109 ASN 4 109 ASN 6 139 ASN A 60 HIS A 125 ASN B 109 ASN B 125 ASN E 109 ASN E 125 ASN F 109 ASN F 125 ASN G 60 HIS G 109 ASN G 125 ASN G 139 ASN H 109 ASN I 60 HIS I 125 ASN K 60 HIS K 125 ASN M 60 HIS M 109 ASN M 139 ASN O 109 ASN O 125 ASN P 60 HIS P 109 ASN Q 109 ASN Q 125 ASN Q 139 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN Y 60 HIS Y 109 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN r 60 HIS r 109 ASN r 125 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.162980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.155347 restraints weight = 19638.831| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.32 r_work: 0.3394 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3023 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34776 Z= 0.194 Angle : 0.726 6.442 46848 Z= 0.379 Chirality : 0.044 0.164 4920 Planarity : 0.005 0.033 6192 Dihedral : 4.632 18.749 4536 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.70 (0.13), residues: 4032 helix: 2.73 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.24 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 63 TYR 0.052 0.005 TYR G 32 PHE 0.019 0.003 PHE e 41 TRP 0.014 0.003 TRP B 93 HIS 0.010 0.002 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00409 (34776) covalent geometry : angle 0.72621 (46848) hydrogen bonds : bond 0.05568 ( 2688) hydrogen bonds : angle 4.01858 ( 8064) *********************** 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 656 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 655 time to evaluate : 1.080 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 655 average time/residue: 0.8024 time to fit residues: 604.1746 Evaluate side-chains 570 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 123 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 289 optimal weight: 7.9990 chunk 380 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 1 139 ASN 2 109 ASN 2 139 ASN 4 109 ASN 4 139 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 125 ASN E 139 ASN F 109 ASN F 125 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 60 HIS H 109 ASN H 139 ASN I 125 ASN I 139 ASN K 125 ASN K 139 ASN M 109 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 139 ASN U 125 ASN U 139 ASN W 109 ASN W 125 ASN W 139 ASN X 125 ASN X 139 ASN Y 109 ASN Y 139 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.162875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.155207 restraints weight = 19620.400| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.31 r_work: 0.3392 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3025 rms_B_bonded: 3.18 restraints_weight: 0.1250 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34776 Z= 0.199 Angle : 0.722 7.009 46848 Z= 0.378 Chirality : 0.042 0.161 4920 Planarity : 0.005 0.037 6192 Dihedral : 4.621 17.716 4536 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.59 (0.13), residues: 4032 helix: 2.67 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.06 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 22 TYR 0.033 0.004 TYR A 32 PHE 0.018 0.003 PHE 1 41 TRP 0.015 0.004 TRP Y 93 HIS 0.010 0.002 HIS F 128 Details of bonding type rmsd covalent geometry : bond 0.00423 (34776) covalent geometry : angle 0.72239 (46848) hydrogen bonds : bond 0.05620 ( 2688) hydrogen bonds : angle 4.02839 ( 8064) *********************** 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 644 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 641 time to evaluate : 1.153 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 641 average time/residue: 0.8105 time to fit residues: 596.9871 Evaluate side-chains 559 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 108 optimal weight: 8.9990 chunk 301 optimal weight: 0.6980 chunk 382 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 263 optimal weight: 0.0270 chunk 304 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 280 optimal weight: 8.9990 chunk 274 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 139 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 139 ASN F 109 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 ASN H 139 ASN I 125 ASN I 139 ASN K 125 ASN K 139 ASN M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 139 ASN S 125 ASN S 139 ASN U 125 ASN U 139 ASN W 109 ASN W 125 ASN W 139 ASN X 125 ASN X 139 ASN Y 60 HIS Y 109 ASN Y 125 ASN Y 139 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.167312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.159677 restraints weight = 19709.317| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 0.32 r_work: 0.3445 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3079 rms_B_bonded: 3.20 restraints_weight: 0.1250 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 34776 Z= 0.119 Angle : 0.551 6.501 46848 Z= 0.289 Chirality : 0.036 0.143 4920 Planarity : 0.003 0.016 6192 Dihedral : 4.379 23.788 4536 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.41 (0.13), residues: 4032 helix: 3.28 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.11 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.016 0.002 TYR A 32 PHE 0.013 0.002 PHE A 41 TRP 0.012 0.002 TRP X 93 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00238 (34776) covalent geometry : angle 0.55063 (46848) hydrogen bonds : bond 0.04347 ( 2688) hydrogen bonds : angle 3.67069 ( 8064) *********************** 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 604 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 599 time to evaluate : 1.266 Fit side-chains REVERT: 1 86 GLN cc_start: 0.7942 (mm110) cc_final: 0.7139 (pm20) REVERT: 2 86 GLN cc_start: 0.7953 (mm110) cc_final: 0.7160 (pm20) REVERT: 4 86 GLN cc_start: 0.7962 (mm110) cc_final: 0.7165 (pm20) REVERT: A 86 GLN cc_start: 0.7949 (mm110) cc_final: 0.7149 (pm20) REVERT: B 86 GLN cc_start: 0.7944 (mm110) cc_final: 0.7146 (pm20) REVERT: F 86 GLN cc_start: 0.7963 (mm110) cc_final: 0.7161 (pm20) REVERT: G 86 GLN cc_start: 0.7967 (mm110) cc_final: 0.7160 (pm20) REVERT: H 86 GLN cc_start: 0.7964 (mm110) cc_final: 0.7157 (pm20) REVERT: I 86 GLN cc_start: 0.7938 (mm110) cc_final: 0.7132 (pm20) REVERT: K 86 GLN cc_start: 0.7930 (mm110) cc_final: 0.7128 (pm20) REVERT: M 86 GLN cc_start: 0.7940 (mm110) cc_final: 0.7133 (pm20) REVERT: O 86 GLN cc_start: 0.7930 (mm110) cc_final: 0.7131 (pm20) REVERT: Q 86 GLN cc_start: 0.7952 (mm110) cc_final: 0.7153 (pm20) REVERT: S 86 GLN cc_start: 0.7922 (mm110) cc_final: 0.7139 (pm20) REVERT: U 86 GLN cc_start: 0.7925 (mm110) cc_final: 0.7124 (pm20) REVERT: W 86 GLN cc_start: 0.7948 (mm110) cc_final: 0.7155 (pm20) REVERT: X 86 GLN cc_start: 0.7937 (mm110) cc_final: 0.7145 (pm20) REVERT: Y 86 GLN cc_start: 0.7969 (mm110) cc_final: 0.7169 (pm20) REVERT: a 86 GLN cc_start: 0.7952 (mm110) cc_final: 0.7163 (pm20) REVERT: e 86 GLN cc_start: 0.7947 (mm110) cc_final: 0.7153 (pm20) REVERT: r 86 GLN cc_start: 0.7952 (mm110) cc_final: 0.7150 (pm20) outliers start: 5 outliers final: 1 residues processed: 599 average time/residue: 0.8710 time to fit residues: 596.6728 Evaluate side-chains 538 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 537 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 30 optimal weight: 0.8980 chunk 283 optimal weight: 0.9990 chunk 323 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 109 ASN 6 139 ASN A 109 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 139 ASN F 109 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 ASN H 139 ASN I 109 ASN I 125 ASN I 139 ASN K 109 ASN K 125 ASN K 139 ASN M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 109 ASN U 125 ASN U 139 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN X 139 ASN Y 109 ASN Y 125 ASN Y 139 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.164496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.156792 restraints weight = 19715.791| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 0.33 r_work: 0.3411 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3040 rms_B_bonded: 3.26 restraints_weight: 0.1250 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34776 Z= 0.159 Angle : 0.632 6.987 46848 Z= 0.332 Chirality : 0.039 0.149 4920 Planarity : 0.004 0.027 6192 Dihedral : 4.536 24.175 4536 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.19 % Allowed : 5.83 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.16 (0.13), residues: 4032 helix: 3.09 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.10 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 22 TYR 0.018 0.003 TYR 6 39 PHE 0.016 0.003 PHE O 41 TRP 0.013 0.003 TRP E 93 HIS 0.008 0.001 HIS 1 128 Details of bonding type rmsd covalent geometry : bond 0.00331 (34776) covalent geometry : angle 0.63204 (46848) hydrogen bonds : bond 0.05089 ( 2688) hydrogen bonds : angle 3.84733 ( 8064) *********************** 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 602 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 595 time to evaluate : 1.384 Fit side-chains REVERT: Y 86 GLN cc_start: 0.8000 (mm110) cc_final: 0.7210 (pm20) outliers start: 7 outliers final: 7 residues processed: 595 average time/residue: 0.8386 time to fit residues: 570.7340 Evaluate side-chains 548 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 541 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain Y residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 188 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 369 optimal weight: 4.9990 chunk 378 optimal weight: 2.9990 chunk 348 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 109 ASN 6 139 ASN A 109 ASN A 125 ASN A 139 ASN B 60 HIS B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 139 ASN F 109 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 60 HIS H 109 ASN H 125 ASN H 139 ASN I 109 ASN I 125 ASN I 139 ASN K 109 ASN K 125 ASN K 139 ASN M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 109 ASN U 125 ASN U 139 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN X 139 ASN Y 109 ASN Y 125 ASN Y 139 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.164015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.156368 restraints weight = 19742.394| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 0.31 r_work: 0.3409 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3039 rms_B_bonded: 3.22 restraints_weight: 0.1250 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34776 Z= 0.181 Angle : 0.675 7.145 46848 Z= 0.354 Chirality : 0.041 0.152 4920 Planarity : 0.004 0.029 6192 Dihedral : 4.567 23.032 4536 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.19 % Allowed : 6.62 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.92 (0.13), residues: 4032 helix: 2.92 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.05 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 22 TYR 0.018 0.003 TYR I 39 PHE 0.018 0.003 PHE W 41 TRP 0.015 0.004 TRP r 93 HIS 0.008 0.002 HIS 2 128 Details of bonding type rmsd covalent geometry : bond 0.00382 (34776) covalent geometry : angle 0.67473 (46848) hydrogen bonds : bond 0.05363 ( 2688) hydrogen bonds : angle 3.92496 ( 8064) *********************** 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 615 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 608 time to evaluate : 1.083 Fit side-chains REVERT: 2 86 GLN cc_start: 0.7986 (mm110) cc_final: 0.7192 (pm20) REVERT: B 86 GLN cc_start: 0.7982 (mm110) cc_final: 0.7184 (pm20) REVERT: F 86 GLN cc_start: 0.8005 (mm110) cc_final: 0.7213 (pm20) REVERT: O 86 GLN cc_start: 0.7984 (mm110) cc_final: 0.7186 (pm20) REVERT: U 86 GLN cc_start: 0.7994 (mm110) cc_final: 0.7191 (pm20) REVERT: X 86 GLN cc_start: 0.7984 (mm110) cc_final: 0.7194 (pm20) REVERT: Y 86 GLN cc_start: 0.8002 (mm110) cc_final: 0.7215 (pm20) REVERT: e 86 GLN cc_start: 0.7996 (mm110) cc_final: 0.7200 (pm20) outliers start: 7 outliers final: 7 residues processed: 608 average time/residue: 0.8551 time to fit residues: 596.7052 Evaluate side-chains 554 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 547 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain Y residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 375 optimal weight: 6.9990 chunk 352 optimal weight: 5.9990 chunk 373 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 406 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 372 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 109 ASN 6 139 ASN A 109 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 139 ASN F 109 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 ASN H 139 ASN I 109 ASN I 125 ASN I 139 ASN K 109 ASN K 125 ASN K 139 ASN M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 109 ASN U 125 ASN U 139 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN X 139 ASN Y 109 ASN Y 125 ASN Y 139 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.168186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.160656 restraints weight = 19928.919| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 0.31 r_work: 0.3460 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3094 rms_B_bonded: 3.25 restraints_weight: 0.1250 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 34776 Z= 0.114 Angle : 0.546 7.212 46848 Z= 0.288 Chirality : 0.036 0.140 4920 Planarity : 0.003 0.015 6192 Dihedral : 4.352 24.840 4536 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.16 % Allowed : 7.43 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.52 (0.13), residues: 4032 helix: 3.39 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.00 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 22 TYR 0.016 0.002 TYR e 39 PHE 0.011 0.002 PHE e 41 TRP 0.012 0.003 TRP I 93 HIS 0.005 0.001 HIS F 128 Details of bonding type rmsd covalent geometry : bond 0.00227 (34776) covalent geometry : angle 0.54576 (46848) hydrogen bonds : bond 0.04218 ( 2688) hydrogen bonds : angle 3.64758 ( 8064) *********************** 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 598 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 592 time to evaluate : 1.471 Fit side-chains REVERT: 1 70 MET cc_start: 0.8199 (mtp) cc_final: 0.7994 (mtp) REVERT: 1 86 GLN cc_start: 0.7937 (mm110) cc_final: 0.7134 (pm20) REVERT: 2 70 MET cc_start: 0.8202 (mtp) cc_final: 0.7995 (mtp) REVERT: 2 86 GLN cc_start: 0.7925 (mm110) cc_final: 0.7126 (pm20) REVERT: 4 70 MET cc_start: 0.8204 (mtp) cc_final: 0.8000 (mtp) REVERT: 4 86 GLN cc_start: 0.7954 (mm110) cc_final: 0.7150 (pm20) REVERT: 6 86 GLN cc_start: 0.7962 (mm110) cc_final: 0.7168 (pm20) REVERT: A 70 MET cc_start: 0.8197 (mtp) cc_final: 0.7995 (mtp) REVERT: A 86 GLN cc_start: 0.7930 (mm110) cc_final: 0.7129 (pm20) REVERT: B 70 MET cc_start: 0.8207 (mtp) cc_final: 0.8005 (mtp) REVERT: B 86 GLN cc_start: 0.7916 (mm110) cc_final: 0.7112 (pm20) REVERT: E 70 MET cc_start: 0.8200 (mtp) cc_final: 0.7997 (mtp) REVERT: F 70 MET cc_start: 0.8189 (mtp) cc_final: 0.7979 (mtp) REVERT: F 86 GLN cc_start: 0.7941 (mm110) cc_final: 0.7121 (pm20) REVERT: G 70 MET cc_start: 0.8181 (mtp) cc_final: 0.7980 (mtp) REVERT: G 86 GLN cc_start: 0.7973 (mm110) cc_final: 0.7158 (pm20) REVERT: H 70 MET cc_start: 0.8192 (mtp) cc_final: 0.7986 (mtp) REVERT: H 86 GLN cc_start: 0.7937 (mm110) cc_final: 0.7124 (pm20) REVERT: I 70 MET cc_start: 0.8195 (mtp) cc_final: 0.7990 (mtp) REVERT: I 86 GLN cc_start: 0.7948 (mm110) cc_final: 0.7137 (pm20) REVERT: K 70 MET cc_start: 0.8203 (mtp) cc_final: 0.7998 (mtp) REVERT: K 86 GLN cc_start: 0.7936 (mm110) cc_final: 0.7126 (pm20) REVERT: M 86 GLN cc_start: 0.7932 (mm110) cc_final: 0.7125 (pm20) REVERT: O 70 MET cc_start: 0.8200 (mtp) cc_final: 0.7988 (mtp) REVERT: O 86 GLN cc_start: 0.7921 (mm110) cc_final: 0.7115 (pm20) REVERT: P 70 MET cc_start: 0.8193 (mtp) cc_final: 0.7985 (mtp) REVERT: Q 86 GLN cc_start: 0.7950 (mm110) cc_final: 0.7148 (pm20) REVERT: S 70 MET cc_start: 0.8188 (mtp) cc_final: 0.7981 (mtp) REVERT: S 86 GLN cc_start: 0.7931 (mm110) cc_final: 0.7143 (pm20) REVERT: U 70 MET cc_start: 0.8181 (mtp) cc_final: 0.7973 (mtp) REVERT: U 86 GLN cc_start: 0.7931 (mm110) cc_final: 0.7118 (pm20) REVERT: W 70 MET cc_start: 0.8175 (mtp) cc_final: 0.7968 (mtp) REVERT: W 86 GLN cc_start: 0.7944 (mm110) cc_final: 0.7138 (pm20) REVERT: X 70 MET cc_start: 0.8197 (mtp) cc_final: 0.7985 (mtp) REVERT: X 86 GLN cc_start: 0.7930 (mm110) cc_final: 0.7125 (pm20) REVERT: Y 70 MET cc_start: 0.8199 (mtp) cc_final: 0.7994 (mtp) REVERT: Y 86 GLN cc_start: 0.7942 (mm110) cc_final: 0.7140 (pm20) REVERT: a 86 GLN cc_start: 0.7963 (mm110) cc_final: 0.7166 (pm20) REVERT: e 70 MET cc_start: 0.8195 (mtp) cc_final: 0.7989 (mtp) REVERT: e 86 GLN cc_start: 0.7951 (mm110) cc_final: 0.7141 (pm20) REVERT: r 70 MET cc_start: 0.8200 (mtp) cc_final: 0.8000 (mtp) REVERT: r 86 GLN cc_start: 0.7940 (mm110) cc_final: 0.7135 (pm20) outliers start: 6 outliers final: 0 residues processed: 598 average time/residue: 0.9163 time to fit residues: 626.0527 Evaluate side-chains 559 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 135 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 373 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 57 HIS 6 109 ASN 6 139 ASN A 109 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 139 ASN F 57 HIS F 109 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 ASN H 139 ASN I 109 ASN I 125 ASN I 139 ASN K 109 ASN K 125 ASN K 139 ASN M 57 HIS M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 109 ASN U 125 ASN U 139 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN X 139 ASN Y 109 ASN Y 125 ASN Y 139 ASN a 57 HIS a 109 ASN a 125 ASN a 139 ASN e 57 HIS e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.163618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.156002 restraints weight = 19746.871| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 0.31 r_work: 0.3405 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3036 rms_B_bonded: 3.20 restraints_weight: 0.1250 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 34776 Z= 0.209 Angle : 0.725 7.978 46848 Z= 0.380 Chirality : 0.043 0.159 4920 Planarity : 0.004 0.034 6192 Dihedral : 4.554 21.205 4536 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.19 % Allowed : 7.76 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.13), residues: 4032 helix: 2.84 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.05 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 22 TYR 0.018 0.003 TYR O 39 PHE 0.019 0.003 PHE W 41 TRP 0.015 0.004 TRP E 93 HIS 0.009 0.002 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00445 (34776) covalent geometry : angle 0.72529 (46848) hydrogen bonds : bond 0.05659 ( 2688) hydrogen bonds : angle 3.99334 ( 8064) *********************** 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 611 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 604 time to evaluate : 0.988 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 604 average time/residue: 0.8507 time to fit residues: 588.3552 Evaluate side-chains 560 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 108 optimal weight: 0.9980 chunk 405 optimal weight: 6.9990 chunk 375 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 chunk 392 optimal weight: 4.9990 chunk 329 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 57 HIS 1 109 ASN 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 57 HIS 6 109 ASN 6 139 ASN A 57 HIS A 109 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 139 ASN F 57 HIS F 109 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 ASN H 139 ASN I 109 ASN I 125 ASN I 139 ASN K 109 ASN K 125 ASN K 139 ASN M 57 HIS M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 109 ASN U 125 ASN U 139 ASN W 57 HIS W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN X 139 ASN Y 109 ASN Y 125 ASN Y 139 ASN a 57 HIS a 109 ASN a 125 ASN a 139 ASN e 57 HIS e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.164095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.156519 restraints weight = 19748.337| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 0.31 r_work: 0.3413 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.3046 rms_B_bonded: 3.18 restraints_weight: 0.1250 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 34776 Z= 0.187 Angle : 0.699 8.132 46848 Z= 0.368 Chirality : 0.042 0.157 4920 Planarity : 0.004 0.030 6192 Dihedral : 4.566 21.148 4536 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.13), residues: 4032 helix: 2.80 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 0.99 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 22 TYR 0.019 0.003 TYR E 39 PHE 0.018 0.003 PHE H 41 TRP 0.015 0.003 TRP M 93 HIS 0.008 0.002 HIS I 128 Details of bonding type rmsd covalent geometry : bond 0.00394 (34776) covalent geometry : angle 0.69894 (46848) hydrogen bonds : bond 0.05423 ( 2688) hydrogen bonds : angle 3.95912 ( 8064) *********************** 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 604 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 1.160 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.8455 time to fit residues: 586.1825 Evaluate side-chains 545 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 157 optimal weight: 9.9990 chunk 392 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 360 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 271 optimal weight: 0.9990 chunk 335 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 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 57 HIS 1 109 ASN 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 57 HIS 6 109 ASN 6 139 ASN A 57 HIS A 109 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 139 ASN F 57 HIS F 109 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 ASN H 139 ASN I 109 ASN I 125 ASN I 139 ASN K 57 HIS K 109 ASN K 125 ASN K 139 ASN M 57 HIS M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 109 ASN U 125 ASN U 139 ASN W 57 HIS W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN X 139 ASN Y 109 ASN Y 125 ASN Y 139 ASN a 57 HIS a 109 ASN a 125 ASN a 139 ASN e 57 HIS e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.164611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.157045 restraints weight = 19866.648| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 0.31 r_work: 0.3420 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3052 rms_B_bonded: 3.20 restraints_weight: 0.1250 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.004 0.026 34776 Z= 0.175 Angle : 0.687 9.031 46848 Z= 0.363 Chirality : 0.041 0.155 4920 Planarity : 0.004 0.027 6192 Dihedral : 4.554 21.568 4536 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.16 % Allowed : 7.87 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.81 (0.13), residues: 4032 helix: 2.85 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 0.99 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 22 TYR 0.018 0.003 TYR E 39 PHE 0.017 0.003 PHE I 41 TRP 0.014 0.003 TRP K 93 HIS 0.008 0.001 HIS X 128 Details of bonding type rmsd covalent geometry : bond 0.00368 (34776) covalent geometry : angle 0.68708 (46848) hydrogen bonds : bond 0.05280 ( 2688) hydrogen bonds : angle 3.93961 ( 8064) ********************** 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 606 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 600 time to evaluate : 1.328 Fit side-chains REVERT: Y 86 GLN cc_start: 0.8009 (mm110) cc_final: 0.7212 (pm20) outliers start: 6 outliers final: 6 residues processed: 600 average time/residue: 0.8307 time to fit residues: 572.3375 Evaluate side-chains 552 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 546 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain Y residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 229 optimal weight: 0.8980 chunk 309 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 406 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 57 HIS 1 109 ASN 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 57 HIS 6 109 ASN 6 139 ASN A 57 HIS A 109 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 109 ASN E 139 ASN F 57 HIS F 109 ASN F 139 ASN G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 ASN H 139 ASN I 109 ASN I 125 ASN I 139 ASN K 57 HIS K 109 ASN K 125 ASN K 139 ASN M 57 HIS M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN O 139 ASN P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 139 ASN S 57 HIS S 109 ASN S 125 ASN S 139 ASN U 109 ASN U 125 ASN U 139 ASN W 57 HIS W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN X 139 ASN Y 109 ASN Y 125 ASN Y 139 ASN a 57 HIS a 109 ASN a 125 ASN a 139 ASN e 57 HIS e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.163667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.156109 restraints weight = 19723.097| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 0.31 r_work: 0.3410 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.3044 rms_B_bonded: 3.16 restraints_weight: 0.1250 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 34776 Z= 0.224 Angle : 0.774 9.788 46848 Z= 0.409 Chirality : 0.045 0.171 4920 Planarity : 0.005 0.039 6192 Dihedral : 4.635 19.636 4536 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.16 % Allowed : 8.31 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.13), residues: 4032 helix: 2.60 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.01 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 22 TYR 0.020 0.004 TYR O 39 PHE 0.019 0.004 PHE W 41 TRP 0.017 0.004 TRP O 93 HIS 0.009 0.002 HIS I 128 Details of bonding type rmsd covalent geometry : bond 0.00481 (34776) covalent geometry : angle 0.77415 (46848) hydrogen bonds : bond 0.05850 ( 2688) hydrogen bonds : angle 4.09132 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18314.53 seconds wall clock time: 311 minutes 59.94 seconds (18719.94 seconds total)