Starting phenix.real_space_refine on Sun Jun 29 13:15:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpm_16783/06_2025/8cpm_16783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpm_16783/06_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_16783/06_2025/8cpm_16783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpm_16783/06_2025/8cpm_16783.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpm_16783/06_2025/8cpm_16783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpm_16783/06_2025/8cpm_16783.cif" } resolution = 1.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 21.38, per 1000 atoms: 0.59 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: 9.45 Conformation dependent library (CDL) restraints added in 3.8 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 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: 12.60 Time building geometry restraints manager: 10.79 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: 0.08 Found NCS groups: ncs_group { reference = (chain '1' and (resid 4 through 176 or resid 201)) selection = (chain '2' and (resid 4 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 176 or resid 500)) selection = (chain 'B' and (resid 4 through 176 or resid 500)) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid 4 through 176 or resid 201)) selection = (chain 'H' and (resid 4 through 176 or resid 201)) selection = chain 'I' selection = chain 'K' selection = (chain 'M' and (resid 4 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 176 or resid 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.420 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 76.630 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.620 ------------------------------------------------------------------------------- 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 : 7.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (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 TRP 0.020 0.004 TRP 1 93 HIS 0.015 0.002 HIS E 128 PHE 0.022 0.003 PHE A 41 TYR 0.092 0.007 TYR r 32 ARG 0.012 0.003 ARG 6 9 Details of bonding type rmsd hydrogen bonds : bond 0.06030 ( 2688) hydrogen bonds : angle 4.31313 ( 8064) covalent geometry : bond 0.00525 (34776) covalent geometry : angle 0.84800 (46848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 4.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 1.9560 time to fit residues: 1390.6036 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 : 3.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 208 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 139 ASN Y 109 ASN a 109 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.165581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.157924 restraints weight = 19513.747| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 0.33 r_work: 0.3421 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3054 rms_B_bonded: 3.18 restraints_weight: 0.1250 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34776 Z= 0.146 Angle : 0.626 5.759 46848 Z= 0.329 Chirality : 0.040 0.153 4920 Planarity : 0.004 0.021 6192 Dihedral : 4.493 19.303 4536 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.13), residues: 4032 helix: 3.06 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.28 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 93 HIS 0.008 0.001 HIS r 128 PHE 0.015 0.002 PHE S 41 TYR 0.044 0.003 TYR A 32 ARG 0.004 0.000 ARG S 63 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 2688) hydrogen bonds : angle 3.82396 ( 8064) covalent geometry : bond 0.00299 (34776) covalent geometry : angle 0.62569 (46848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 668 time to evaluate : 4.183 Fit side-chains REVERT: B 86 GLN cc_start: 0.7957 (mm110) cc_final: 0.7188 (pm20) REVERT: S 86 GLN cc_start: 0.7952 (mm110) cc_final: 0.7194 (pm20) outliers start: 1 outliers final: 0 residues processed: 668 average time/residue: 2.0593 time to fit residues: 1585.2746 Evaluate side-chains 554 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 79 optimal weight: 4.9990 chunk 340 optimal weight: 3.9990 chunk 383 optimal weight: 0.6980 chunk 301 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 338 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 4 125 ASN 4 139 ASN 6 125 ASN 6 139 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 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 125 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: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.164643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.156893 restraints weight = 19786.273| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 0.32 r_work: 0.3410 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3043 rms_B_bonded: 3.22 restraints_weight: 0.1250 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34776 Z= 0.147 Angle : 0.605 6.448 46848 Z= 0.321 Chirality : 0.040 0.145 4920 Planarity : 0.004 0.025 6192 Dihedral : 4.548 20.671 4536 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.13), residues: 4032 helix: 3.16 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.24 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP M 93 HIS 0.007 0.001 HIS I 128 PHE 0.015 0.002 PHE 4 41 TYR 0.030 0.003 TYR r 32 ARG 0.003 0.001 ARG X 63 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 2688) hydrogen bonds : angle 3.76418 ( 8064) covalent geometry : bond 0.00303 (34776) covalent geometry : angle 0.60529 (46848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 5.630 Fit side-chains REVERT: 1 60 HIS cc_start: 0.8199 (m-70) cc_final: 0.7968 (m170) REVERT: 2 86 GLN cc_start: 0.7961 (mm110) cc_final: 0.7163 (pm20) REVERT: 4 86 GLN cc_start: 0.7939 (mm110) cc_final: 0.7156 (pm20) REVERT: B 86 GLN cc_start: 0.7960 (mm110) cc_final: 0.7165 (pm20) REVERT: E 86 GLN cc_start: 0.7944 (mm110) cc_final: 0.7150 (pm20) REVERT: M 60 HIS cc_start: 0.8205 (m-70) cc_final: 0.7981 (m170) REVERT: M 86 GLN cc_start: 0.7969 (mm110) cc_final: 0.7170 (pm20) REVERT: O 86 GLN cc_start: 0.7956 (mm110) cc_final: 0.7159 (pm20) REVERT: S 86 GLN cc_start: 0.7977 (mm110) cc_final: 0.7198 (pm20) REVERT: U 86 GLN cc_start: 0.7955 (mm110) cc_final: 0.7156 (pm20) REVERT: X 86 GLN cc_start: 0.7957 (mm110) cc_final: 0.7165 (pm20) REVERT: Y 86 GLN cc_start: 0.7983 (mm110) cc_final: 0.7185 (pm20) REVERT: e 86 GLN cc_start: 0.7964 (mm110) cc_final: 0.7181 (pm20) REVERT: r 60 HIS cc_start: 0.8199 (m-70) cc_final: 0.7974 (m170) outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 2.2436 time to fit residues: 1609.8294 Evaluate side-chains 549 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 549 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 91 optimal weight: 6.9990 chunk 341 optimal weight: 6.9990 chunk 349 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 386 optimal weight: 2.9990 chunk 327 optimal weight: 8.9990 chunk 318 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 125 ASN 6 139 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 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 139 ASN Q 109 ASN Q 125 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 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: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.163260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.155451 restraints weight = 19636.520| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.32 r_work: 0.3394 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3026 rms_B_bonded: 3.17 restraints_weight: 0.1250 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 34776 Z= 0.182 Angle : 0.667 6.371 46848 Z= 0.353 Chirality : 0.041 0.155 4920 Planarity : 0.004 0.035 6192 Dihedral : 4.600 21.210 4536 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.19 % Allowed : 5.17 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.13), residues: 4032 helix: 2.91 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.12 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP U 93 HIS 0.009 0.002 HIS B 128 PHE 0.018 0.003 PHE G 41 TYR 0.026 0.003 TYR A 32 ARG 0.004 0.001 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.05467 ( 2688) hydrogen bonds : angle 3.87700 ( 8064) covalent geometry : bond 0.00385 (34776) covalent geometry : angle 0.66700 (46848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 594 time to evaluate : 4.200 Fit side-chains REVERT: 2 86 GLN cc_start: 0.7987 (mm110) cc_final: 0.7188 (pm20) REVERT: B 86 GLN cc_start: 0.7961 (mm110) cc_final: 0.7166 (pm20) REVERT: O 86 GLN cc_start: 0.7960 (mm110) cc_final: 0.7165 (pm20) REVERT: S 86 GLN cc_start: 0.7957 (mm110) cc_final: 0.7171 (pm20) REVERT: X 86 GLN cc_start: 0.7986 (mm110) cc_final: 0.7196 (pm20) REVERT: Y 86 GLN cc_start: 0.7994 (mm110) cc_final: 0.7200 (pm20) outliers start: 7 outliers final: 5 residues processed: 594 average time/residue: 2.1278 time to fit residues: 1456.4772 Evaluate side-chains 550 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 545 time to evaluate : 4.096 ------------------------------------------------------------------------------- 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 Y residue 91 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 1 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 323 optimal weight: 5.9990 chunk 364 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 125 ASN 6 139 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 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 139 ASN Q 109 ASN Q 125 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: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.164083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.156322 restraints weight = 19755.804| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 0.31 r_work: 0.3403 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3034 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1265 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= 0.160 Angle : 0.618 6.300 46848 Z= 0.328 Chirality : 0.039 0.149 4920 Planarity : 0.004 0.025 6192 Dihedral : 4.513 21.668 4536 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.46 % Allowed : 6.07 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.13), residues: 4032 helix: 3.03 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.12 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP U 93 HIS 0.007 0.001 HIS 4 128 PHE 0.015 0.003 PHE e 41 TYR 0.020 0.003 TYR 2 39 ARG 0.004 0.001 ARG 6 22 Details of bonding type rmsd hydrogen bonds : bond 0.05122 ( 2688) hydrogen bonds : angle 3.78660 ( 8064) covalent geometry : bond 0.00333 (34776) covalent geometry : angle 0.61803 (46848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 592 time to evaluate : 4.092 Fit side-chains REVERT: 2 86 GLN cc_start: 0.7974 (mm110) cc_final: 0.7165 (pm20) REVERT: 4 86 GLN cc_start: 0.7964 (mm110) cc_final: 0.7161 (pm20) REVERT: B 86 GLN cc_start: 0.7959 (mm110) cc_final: 0.7158 (pm20) REVERT: E 86 GLN cc_start: 0.7966 (mm110) cc_final: 0.7160 (pm20) REVERT: F 86 GLN cc_start: 0.7985 (mm110) cc_final: 0.7181 (pm20) REVERT: M 86 GLN cc_start: 0.7987 (mm110) cc_final: 0.7182 (pm20) REVERT: O 86 GLN cc_start: 0.7956 (mm110) cc_final: 0.7153 (pm20) REVERT: S 86 GLN cc_start: 0.7960 (mm110) cc_final: 0.7165 (pm20) REVERT: U 86 GLN cc_start: 0.7972 (mm110) cc_final: 0.7170 (pm20) REVERT: X 86 GLN cc_start: 0.7980 (mm110) cc_final: 0.7182 (pm20) REVERT: Y 86 GLN cc_start: 0.7991 (mm110) cc_final: 0.7190 (pm20) REVERT: e 86 GLN cc_start: 0.7982 (mm110) cc_final: 0.7186 (pm20) outliers start: 17 outliers final: 7 residues processed: 592 average time/residue: 2.0790 time to fit residues: 1414.5675 Evaluate side-chains 552 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 545 time to evaluate : 4.241 ------------------------------------------------------------------------------- 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 185 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 335 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 353 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 376 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN 6 139 ASN A 125 ASN A 139 ASN B 60 HIS 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 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 139 ASN Q 109 ASN Q 125 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 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: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.163657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.155897 restraints weight = 19745.607| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 0.32 r_work: 0.3398 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3029 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34776 Z= 0.167 Angle : 0.637 6.234 46848 Z= 0.337 Chirality : 0.039 0.153 4920 Planarity : 0.004 0.030 6192 Dihedral : 4.522 21.076 4536 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.19 % Allowed : 6.67 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.01 (0.13), residues: 4032 helix: 3.00 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.04 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP U 93 HIS 0.007 0.001 HIS r 128 PHE 0.016 0.003 PHE I 41 TYR 0.021 0.003 TYR G 39 ARG 0.004 0.001 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.05249 ( 2688) hydrogen bonds : angle 3.81728 ( 8064) covalent geometry : bond 0.00351 (34776) covalent geometry : angle 0.63671 (46848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 595 time to evaluate : 3.831 Fit side-chains REVERT: 2 86 GLN cc_start: 0.7971 (mm110) cc_final: 0.7169 (pm20) REVERT: B 86 GLN cc_start: 0.7957 (mm110) cc_final: 0.7158 (pm20) REVERT: E 86 GLN cc_start: 0.7967 (mm110) cc_final: 0.7161 (pm20) REVERT: F 86 GLN cc_start: 0.7995 (mm110) cc_final: 0.7194 (pm20) REVERT: M 86 GLN cc_start: 0.7988 (mm110) cc_final: 0.7185 (pm20) REVERT: O 86 GLN cc_start: 0.7965 (mm110) cc_final: 0.7164 (pm20) REVERT: S 86 GLN cc_start: 0.7960 (mm110) cc_final: 0.7168 (pm20) REVERT: U 86 GLN cc_start: 0.7973 (mm110) cc_final: 0.7173 (pm20) REVERT: X 86 GLN cc_start: 0.7984 (mm110) cc_final: 0.7185 (pm20) REVERT: Y 86 GLN cc_start: 0.7998 (mm110) cc_final: 0.7201 (pm20) REVERT: e 86 GLN cc_start: 0.7982 (mm110) cc_final: 0.7186 (pm20) outliers start: 7 outliers final: 7 residues processed: 595 average time/residue: 2.1729 time to fit residues: 1501.8711 Evaluate side-chains 552 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 545 time to evaluate : 4.204 ------------------------------------------------------------------------------- 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 72 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 4 125 ASN 4 139 ASN 6 139 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 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 139 ASN Q 109 ASN Q 125 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 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: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.162883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.155105 restraints weight = 19824.383| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 0.31 r_work: 0.3390 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3019 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34776 Z= 0.208 Angle : 0.708 6.352 46848 Z= 0.373 Chirality : 0.042 0.157 4920 Planarity : 0.005 0.035 6192 Dihedral : 4.567 19.179 4536 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.19 % Allowed : 6.32 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.13), residues: 4032 helix: 2.83 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.00 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP E 93 HIS 0.009 0.002 HIS E 128 PHE 0.019 0.003 PHE W 41 TYR 0.023 0.003 TYR I 39 ARG 0.005 0.001 ARG S 22 Details of bonding type rmsd hydrogen bonds : bond 0.05726 ( 2688) hydrogen bonds : angle 3.93518 ( 8064) covalent geometry : bond 0.00443 (34776) covalent geometry : angle 0.70823 (46848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 616 time to evaluate : 4.077 Fit side-chains REVERT: B 86 GLN cc_start: 0.7956 (mm110) cc_final: 0.7158 (pm20) REVERT: O 86 GLN cc_start: 0.7957 (mm110) cc_final: 0.7160 (pm20) REVERT: S 86 GLN cc_start: 0.7965 (mm110) cc_final: 0.7181 (pm20) REVERT: X 86 GLN cc_start: 0.7985 (mm110) cc_final: 0.7190 (pm20) REVERT: Y 86 GLN cc_start: 0.7984 (mm110) cc_final: 0.7186 (pm20) outliers start: 7 outliers final: 7 residues processed: 616 average time/residue: 2.0461 time to fit residues: 1446.7562 Evaluate side-chains 575 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 568 time to evaluate : 4.277 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 54 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 384 optimal weight: 6.9990 chunk 266 optimal weight: 0.6980 chunk 281 optimal weight: 0.9980 chunk 328 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 109 ASN 2 125 ASN 4 109 ASN 4 125 ASN 6 139 ASN A 125 ASN B 109 ASN B 125 ASN E 109 ASN E 125 ASN F 109 ASN F 125 ASN G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 ASN I 125 ASN K 125 ASN M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN P 109 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 125 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN X 125 ASN Y 109 ASN Y 125 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN r 109 ASN r 125 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.168410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.160862 restraints weight = 19962.385| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 0.31 r_work: 0.3459 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3095 rms_B_bonded: 3.27 restraints_weight: 0.1250 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 34776 Z= 0.106 Angle : 0.507 6.051 46848 Z= 0.270 Chirality : 0.035 0.142 4920 Planarity : 0.003 0.016 6192 Dihedral : 4.278 22.733 4536 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.72 (0.13), residues: 4032 helix: 3.53 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.06 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 93 HIS 0.005 0.001 HIS G 128 PHE 0.010 0.002 PHE S 41 TYR 0.016 0.002 TYR W 39 ARG 0.002 0.000 ARG S 63 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 2688) hydrogen bonds : angle 3.52834 ( 8064) covalent geometry : bond 0.00206 (34776) covalent geometry : angle 0.50702 (46848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 4.162 Fit side-chains REVERT: 1 86 GLN cc_start: 0.7927 (mm110) cc_final: 0.7115 (pm20) REVERT: 2 86 GLN cc_start: 0.7937 (mm110) cc_final: 0.7127 (pm20) REVERT: 4 86 GLN cc_start: 0.7918 (mm110) cc_final: 0.7110 (pm20) REVERT: 6 86 GLN cc_start: 0.7924 (mm110) cc_final: 0.7127 (pm20) REVERT: A 86 GLN cc_start: 0.7914 (mm110) cc_final: 0.7107 (pm20) REVERT: B 86 GLN cc_start: 0.7943 (mm110) cc_final: 0.7130 (pm20) REVERT: E 86 GLN cc_start: 0.7937 (mm110) cc_final: 0.7123 (pm20) REVERT: F 86 GLN cc_start: 0.7975 (mm110) cc_final: 0.7164 (pm20) REVERT: G 86 GLN cc_start: 0.7941 (mm110) cc_final: 0.7127 (pm20) REVERT: H 86 GLN cc_start: 0.7959 (mm110) cc_final: 0.7137 (pm20) REVERT: I 86 GLN cc_start: 0.7941 (mm110) cc_final: 0.7129 (pm20) REVERT: K 86 GLN cc_start: 0.7954 (mm110) cc_final: 0.7141 (pm20) REVERT: M 86 GLN cc_start: 0.7954 (mm110) cc_final: 0.7138 (pm20) REVERT: O 86 GLN cc_start: 0.7935 (mm110) cc_final: 0.7125 (pm20) REVERT: P 86 GLN cc_start: 0.7969 (mm110) cc_final: 0.7152 (pm20) REVERT: Q 86 GLN cc_start: 0.7927 (mm110) cc_final: 0.7122 (pm20) REVERT: S 86 GLN cc_start: 0.7950 (mm110) cc_final: 0.7154 (pm20) REVERT: U 86 GLN cc_start: 0.7936 (mm110) cc_final: 0.7120 (pm20) REVERT: W 86 GLN cc_start: 0.7934 (mm110) cc_final: 0.7134 (pm20) REVERT: X 86 GLN cc_start: 0.7948 (mm110) cc_final: 0.7132 (pm20) REVERT: Y 86 GLN cc_start: 0.7973 (mm110) cc_final: 0.7168 (pm20) REVERT: a 86 GLN cc_start: 0.7944 (mm110) cc_final: 0.7141 (pm20) REVERT: e 86 GLN cc_start: 0.7958 (mm110) cc_final: 0.7144 (pm20) REVERT: r 86 GLN cc_start: 0.7930 (mm110) cc_final: 0.7124 (pm20) outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 2.0373 time to fit residues: 1428.1738 Evaluate side-chains 536 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 27 optimal weight: 2.9990 chunk 406 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 331 optimal weight: 2.9990 chunk 328 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 125 ASN E 139 ASN F 57 HIS F 109 ASN F 125 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 125 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: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.165804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.158176 restraints weight = 19911.452| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 0.31 r_work: 0.3427 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.3057 rms_B_bonded: 3.23 restraints_weight: 0.1250 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34776 Z= 0.130 Angle : 0.557 6.373 46848 Z= 0.296 Chirality : 0.037 0.143 4920 Planarity : 0.003 0.016 6192 Dihedral : 4.357 21.664 4536 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.13), residues: 4032 helix: 3.41 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.03 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP a 93 HIS 0.006 0.001 HIS F 128 PHE 0.013 0.002 PHE Q 41 TYR 0.018 0.002 TYR X 39 ARG 0.002 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 2688) hydrogen bonds : angle 3.64241 ( 8064) covalent geometry : bond 0.00263 (34776) covalent geometry : angle 0.55729 (46848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 595 time to evaluate : 3.952 Fit side-chains REVERT: 1 86 GLN cc_start: 0.7956 (mm110) cc_final: 0.7149 (pm20) REVERT: 2 86 GLN cc_start: 0.7957 (mm110) cc_final: 0.7160 (pm20) REVERT: 4 86 GLN cc_start: 0.7953 (mm110) cc_final: 0.7154 (pm20) REVERT: 6 86 GLN cc_start: 0.7948 (mm110) cc_final: 0.7159 (pm20) REVERT: A 86 GLN cc_start: 0.7946 (mm110) cc_final: 0.7152 (pm20) REVERT: B 86 GLN cc_start: 0.7948 (mm110) cc_final: 0.7144 (pm20) REVERT: E 86 GLN cc_start: 0.7962 (mm110) cc_final: 0.7156 (pm20) REVERT: F 86 GLN cc_start: 0.7995 (mm110) cc_final: 0.7190 (pm20) REVERT: G 86 GLN cc_start: 0.7964 (mm110) cc_final: 0.7162 (pm20) REVERT: H 86 GLN cc_start: 0.7958 (mm110) cc_final: 0.7148 (pm20) REVERT: I 86 GLN cc_start: 0.7938 (mm110) cc_final: 0.7135 (pm20) REVERT: M 86 GLN cc_start: 0.7970 (mm110) cc_final: 0.7170 (pm20) REVERT: O 86 GLN cc_start: 0.7931 (mm110) cc_final: 0.7127 (pm20) REVERT: P 86 GLN cc_start: 0.7966 (mm110) cc_final: 0.7157 (pm20) REVERT: Q 86 GLN cc_start: 0.7948 (mm110) cc_final: 0.7153 (pm20) REVERT: S 86 GLN cc_start: 0.7940 (mm110) cc_final: 0.7151 (pm20) REVERT: W 86 GLN cc_start: 0.7968 (mm110) cc_final: 0.7180 (pm20) REVERT: X 86 GLN cc_start: 0.7967 (mm110) cc_final: 0.7173 (pm20) REVERT: Y 86 GLN cc_start: 0.7981 (mm110) cc_final: 0.7190 (pm20) REVERT: a 86 GLN cc_start: 0.7971 (mm110) cc_final: 0.7173 (pm20) REVERT: e 86 GLN cc_start: 0.7979 (mm110) cc_final: 0.7176 (pm20) REVERT: r 86 GLN cc_start: 0.7963 (mm110) cc_final: 0.7173 (pm20) outliers start: 6 outliers final: 0 residues processed: 595 average time/residue: 2.0326 time to fit residues: 1386.1227 Evaluate side-chains 557 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 394 optimal weight: 10.0000 chunk 323 optimal weight: 2.9990 chunk 334 optimal weight: 0.9990 chunk 289 optimal weight: 4.9990 chunk 369 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 406 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 375 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 125 ASN E 139 ASN F 109 ASN F 125 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 139 ASN Q 109 ASN Q 125 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 = 0.3628 r_free = 0.3628 target = 0.168009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.160420 restraints weight = 20004.283| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 0.31 r_work: 0.3453 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3087 rms_B_bonded: 3.27 restraints_weight: 0.1250 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 34776 Z= 0.111 Angle : 0.519 5.790 46848 Z= 0.278 Chirality : 0.036 0.140 4920 Planarity : 0.003 0.016 6192 Dihedral : 4.221 20.161 4536 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.79 (0.13), residues: 4032 helix: 3.58 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.03 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 93 HIS 0.005 0.001 HIS r 128 PHE 0.011 0.002 PHE A 41 TYR 0.016 0.002 TYR M 39 ARG 0.002 0.000 ARG 6 63 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 2688) hydrogen bonds : angle 3.51400 ( 8064) covalent geometry : bond 0.00219 (34776) covalent geometry : angle 0.51941 (46848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 3.947 Fit side-chains REVERT: 1 86 GLN cc_start: 0.7935 (mm110) cc_final: 0.7141 (pm20) REVERT: 2 86 GLN cc_start: 0.7969 (mm110) cc_final: 0.7171 (pm20) REVERT: 4 86 GLN cc_start: 0.7936 (mm110) cc_final: 0.7141 (pm20) REVERT: 6 86 GLN cc_start: 0.7942 (mm110) cc_final: 0.7159 (pm20) REVERT: A 86 GLN cc_start: 0.7920 (mm110) cc_final: 0.7132 (pm20) REVERT: B 86 GLN cc_start: 0.7934 (mm110) cc_final: 0.7133 (pm20) REVERT: E 86 GLN cc_start: 0.7949 (mm110) cc_final: 0.7143 (pm20) REVERT: F 86 GLN cc_start: 0.7979 (mm110) cc_final: 0.7180 (pm20) REVERT: G 86 GLN cc_start: 0.7946 (mm110) cc_final: 0.7143 (pm20) REVERT: H 86 GLN cc_start: 0.7947 (mm110) cc_final: 0.7148 (pm20) REVERT: I 86 GLN cc_start: 0.7930 (mm110) cc_final: 0.7130 (pm20) REVERT: K 86 GLN cc_start: 0.7935 (mm110) cc_final: 0.7139 (pm20) REVERT: M 86 GLN cc_start: 0.7965 (mm110) cc_final: 0.7171 (pm20) REVERT: O 86 GLN cc_start: 0.7924 (mm110) cc_final: 0.7126 (pm20) REVERT: P 86 GLN cc_start: 0.7962 (mm110) cc_final: 0.7160 (pm20) REVERT: Q 86 GLN cc_start: 0.7945 (mm110) cc_final: 0.7158 (pm20) REVERT: S 86 GLN cc_start: 0.7923 (mm110) cc_final: 0.7136 (pm20) REVERT: U 86 GLN cc_start: 0.7960 (mm110) cc_final: 0.7160 (pm20) REVERT: W 86 GLN cc_start: 0.7949 (mm110) cc_final: 0.7168 (pm20) REVERT: X 86 GLN cc_start: 0.7966 (mm110) cc_final: 0.7165 (pm20) REVERT: Y 86 GLN cc_start: 0.7967 (mm110) cc_final: 0.7178 (pm20) REVERT: a 86 GLN cc_start: 0.7960 (mm110) cc_final: 0.7172 (pm20) REVERT: e 86 GLN cc_start: 0.7972 (mm110) cc_final: 0.7163 (pm20) REVERT: r 86 GLN cc_start: 0.7950 (mm110) cc_final: 0.7163 (pm20) outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 2.1209 time to fit residues: 1472.9584 Evaluate side-chains 573 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 333 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 382 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 125 ASN E 139 ASN F 57 HIS F 109 ASN F 125 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 139 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 57 HIS 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: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.165094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.157385 restraints weight = 19907.471| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 0.32 r_work: 0.3415 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.3046 rms_B_bonded: 3.25 restraints_weight: 0.1250 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34776 Z= 0.147 Angle : 0.593 7.075 46848 Z= 0.315 Chirality : 0.039 0.143 4920 Planarity : 0.003 0.020 6192 Dihedral : 4.387 20.174 4536 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.13), residues: 4032 helix: 3.32 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.02 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP a 93 HIS 0.007 0.001 HIS I 128 PHE 0.015 0.003 PHE Q 41 TYR 0.019 0.003 TYR E 39 ARG 0.002 0.001 ARG O 76 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 2688) hydrogen bonds : angle 3.70106 ( 8064) covalent geometry : bond 0.00305 (34776) covalent geometry : angle 0.59326 (46848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43925.24 seconds wall clock time: 753 minutes 36.92 seconds (45216.92 seconds total)