Starting phenix.real_space_refine on Sat Mar 23 06:41:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/03_2024/8cpm_16783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/03_2024/8cpm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/03_2024/8cpm_16783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/03_2024/8cpm_16783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/03_2024/8cpm_16783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/03_2024/8cpm_16783_updated.pdb" } 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 Residue "1 ASP 92": "OD1" <-> "OD2" Residue "1 GLU 140": "OE1" <-> "OE2" Residue "2 GLU 140": "OE1" <-> "OE2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 ASP 92": "OD1" <-> "OD2" Residue "4 GLU 140": "OE1" <-> "OE2" Residue "6 ASP 131": "OD1" <-> "OD2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "G ASP 131": "OD1" <-> "OD2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M ASP 131": "OD1" <-> "OD2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "P ASP 92": "OD1" <-> "OD2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "U GLU 64": "OE1" <-> "OE2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "W ASP 131": "OD1" <-> "OD2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "Y GLU 140": "OE1" <-> "OE2" Residue "a ASP 92": "OD1" <-> "OD2" Residue "a ASP 131": "OD1" <-> "OD2" Residue "e ASP 92": "OD1" <-> "OD2" Residue "e GLU 140": "OE1" <-> "OE2" Residue "r ASP 92": "OD1" <-> "OD2" Residue "r GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 17.78, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 15.75 Conformation dependent library (CDL) restraints added in 5.7 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 71.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain '1' and resid 14 through 41 Processing helix chain '1' and resid 49 through 75 Processing helix chain '1' and resid 96 through 123 Processing helix chain '1' and resid 127 through 136 Processing helix chain '1' and resid 138 through 158 Processing helix chain '1' and resid 164 through 173 Processing helix chain '2' and resid 14 through 41 Processing helix chain '2' and resid 49 through 75 Processing helix chain '2' and resid 96 through 123 Processing helix chain '2' and resid 127 through 136 Processing helix chain '2' and resid 138 through 158 Processing helix chain '2' and resid 164 through 173 Processing helix chain '4' and resid 14 through 41 Processing helix chain '4' and resid 49 through 75 Processing helix chain '4' and resid 96 through 123 Processing helix chain '4' and resid 127 through 136 Processing helix chain '4' and resid 138 through 158 Processing helix chain '4' and resid 164 through 173 Processing helix chain '6' and resid 14 through 41 Processing helix chain '6' and resid 49 through 75 Processing helix chain '6' and resid 96 through 123 Processing helix chain '6' and resid 127 through 136 Processing helix chain '6' and resid 138 through 158 Processing helix chain '6' and resid 164 through 173 Processing helix chain 'A' and resid 14 through 41 Processing helix chain 'A' and resid 49 through 75 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 138 through 158 Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'B' and resid 14 through 41 Processing helix chain 'B' and resid 49 through 75 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 138 through 158 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'E' and resid 14 through 41 Processing helix chain 'E' and resid 49 through 75 Processing helix chain 'E' and resid 96 through 123 Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 138 through 158 Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'F' and resid 14 through 41 Processing helix chain 'F' and resid 49 through 75 Processing helix chain 'F' and resid 96 through 123 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 138 through 158 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'G' and resid 14 through 41 Processing helix chain 'G' and resid 49 through 75 Processing helix chain 'G' and resid 96 through 123 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 138 through 158 Processing helix chain 'G' and resid 164 through 173 Processing helix chain 'H' and resid 14 through 41 Processing helix chain 'H' and resid 49 through 75 Processing helix chain 'H' and resid 96 through 123 Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 138 through 158 Processing helix chain 'H' and resid 164 through 173 Processing helix chain 'I' and resid 14 through 41 Processing helix chain 'I' and resid 49 through 75 Processing helix chain 'I' and resid 96 through 123 Processing helix chain 'I' and resid 127 through 136 Processing helix chain 'I' and resid 138 through 158 Processing helix chain 'I' and resid 164 through 173 Processing helix chain 'K' and resid 14 through 41 Processing helix chain 'K' and resid 49 through 75 Processing helix chain 'K' and resid 96 through 123 Processing helix chain 'K' and resid 127 through 136 Processing helix chain 'K' and resid 138 through 158 Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'M' and resid 14 through 41 Processing helix chain 'M' and resid 49 through 75 Processing helix chain 'M' and resid 96 through 123 Processing helix chain 'M' and resid 127 through 136 Processing helix chain 'M' and resid 138 through 158 Processing helix chain 'M' and resid 164 through 173 Processing helix chain 'O' and resid 14 through 41 Processing helix chain 'O' and resid 49 through 75 Processing helix chain 'O' and resid 96 through 123 Processing helix chain 'O' and resid 127 through 136 Processing helix chain 'O' and resid 138 through 158 Processing helix chain 'O' and resid 164 through 173 Processing helix chain 'P' and resid 14 through 41 Processing helix chain 'P' and resid 49 through 75 Processing helix chain 'P' and resid 96 through 123 Processing helix chain 'P' and resid 127 through 136 Processing helix chain 'P' and resid 138 through 158 Processing helix chain 'P' and resid 164 through 173 Processing helix chain 'Q' and resid 14 through 41 Processing helix chain 'Q' and resid 49 through 75 Processing helix chain 'Q' and resid 96 through 123 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 138 through 158 Processing helix chain 'Q' and resid 164 through 173 Processing helix chain 'S' and resid 14 through 41 Processing helix chain 'S' and resid 49 through 75 Processing helix chain 'S' and resid 96 through 123 Processing helix chain 'S' and resid 127 through 136 Processing helix chain 'S' and resid 138 through 158 Processing helix chain 'S' and resid 164 through 173 Processing helix chain 'U' and resid 14 through 41 Processing helix chain 'U' and resid 49 through 75 Processing helix chain 'U' and resid 96 through 123 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'U' and resid 138 through 158 Processing helix chain 'U' and resid 164 through 173 Processing helix chain 'W' and resid 14 through 41 Processing helix chain 'W' and resid 49 through 75 Processing helix chain 'W' and resid 96 through 123 Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 138 through 158 Processing helix chain 'W' and resid 164 through 173 Processing helix chain 'X' and resid 14 through 41 Processing helix chain 'X' and resid 49 through 75 Processing helix chain 'X' and resid 96 through 123 Processing helix chain 'X' and resid 127 through 136 Processing helix chain 'X' and resid 138 through 158 Processing helix chain 'X' and resid 164 through 173 Processing helix chain 'Y' and resid 14 through 41 Processing helix chain 'Y' and resid 49 through 75 Processing helix chain 'Y' and resid 96 through 123 Processing helix chain 'Y' and resid 127 through 136 Processing helix chain 'Y' and resid 138 through 158 Processing helix chain 'Y' and resid 164 through 173 Processing helix chain 'a' and resid 14 through 41 Processing helix chain 'a' and resid 49 through 75 Processing helix chain 'a' and resid 96 through 123 Processing helix chain 'a' and resid 127 through 136 Processing helix chain 'a' and resid 138 through 158 Processing helix chain 'a' and resid 164 through 173 Processing helix chain 'e' and resid 14 through 41 Processing helix chain 'e' and resid 49 through 75 Processing helix chain 'e' and resid 96 through 123 Processing helix chain 'e' and resid 127 through 136 Processing helix chain 'e' and resid 138 through 158 Processing helix chain 'e' and resid 164 through 173 Processing helix chain 'r' and resid 14 through 41 Processing helix chain 'r' and resid 49 through 75 Processing helix chain 'r' and resid 96 through 123 Processing helix chain 'r' and resid 127 through 136 Processing helix chain 'r' and resid 138 through 158 Processing helix chain 'r' and resid 164 through 173 2400 hydrogen bonds defined for protein. 7200 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: 10.95 Time building geometry restraints manager: 16.80 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: 97.00 - 104.39: 353 104.39 - 111.78: 15713 111.78 - 119.17: 12561 119.17 - 126.56: 17830 126.56 - 133.95: 391 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: 30043 3.11 - 3.71: 67720 3.71 - 4.30: 99782 4.30 - 4.90: 155253 Nonbonded interactions: 353983 Sorted by model distance: nonbonded pdb=" O LEU Y 35 " pdb=" O HOH Y 601 " model vdw 1.916 2.440 nonbonded pdb=" O LEU 6 35 " pdb=" O HOH 6 301 " model vdw 1.916 2.440 nonbonded pdb=" O LEU S 35 " pdb=" O HOH S 601 " model vdw 1.917 2.440 nonbonded pdb=" O LEU K 35 " pdb=" O HOH K 601 " model vdw 1.917 2.440 nonbonded pdb=" O LEU G 35 " pdb=" O HOH G 301 " model vdw 1.917 2.440 ... (remaining 353978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 8.920 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 90.580 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.400 ------------------------------------------------------------------------------- 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= 0.342 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 4.302 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 1.9012 time to fit residues: 1351.6378 Evaluate side-chains 562 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 4.007 ------------------------------------------------------------------------------- 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: 7.9990 chunk 171 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 2 60 HIS 2 109 ASN 4 109 ASN 6 139 ASN A 60 HIS A 125 ASN B 109 ASN B 125 ASN E 109 ASN E 125 ASN F 109 ASN F 125 ASN G 60 HIS G 109 ASN G 125 ASN G 139 ASN H 109 ASN I 60 HIS I 125 ASN K 60 HIS K 125 ASN M 60 HIS M 109 ASN M 139 ASN O 109 ASN O 125 ASN P 60 HIS P 109 ASN Q 109 ASN Q 125 ASN Q 139 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN Y 109 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN r 60 HIS r 109 ASN r 125 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 34776 Z= 0.132 Angle : 0.504 6.211 46848 Z= 0.265 Chirality : 0.035 0.137 4920 Planarity : 0.003 0.019 6192 Dihedral : 4.221 19.110 4536 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.13), residues: 4032 helix: 3.58 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.46 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 93 HIS 0.005 0.001 HIS I 128 PHE 0.012 0.002 PHE A 41 TYR 0.034 0.003 TYR A 32 ARG 0.002 0.000 ARG 4 63 *********************** 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 590 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 589 time to evaluate : 4.351 Fit side-chains REVERT: 2 86 GLN cc_start: 0.7461 (mm110) cc_final: 0.6970 (pm20) REVERT: 6 131 ASP cc_start: 0.7208 (t70) cc_final: 0.6745 (t70) REVERT: B 86 GLN cc_start: 0.7468 (mm110) cc_final: 0.6960 (pm20) REVERT: E 86 GLN cc_start: 0.7466 (mm110) cc_final: 0.6961 (pm20) REVERT: F 86 GLN cc_start: 0.7476 (mm110) cc_final: 0.6968 (pm20) REVERT: G 131 ASP cc_start: 0.7209 (t70) cc_final: 0.6751 (t70) REVERT: M 86 GLN cc_start: 0.7459 (mm110) cc_final: 0.6971 (pm20) REVERT: O 86 GLN cc_start: 0.7461 (mm110) cc_final: 0.6960 (pm20) REVERT: Q 131 ASP cc_start: 0.7205 (t70) cc_final: 0.6750 (t70) REVERT: S 86 GLN cc_start: 0.7457 (mm110) cc_final: 0.6976 (pm20) REVERT: U 86 GLN cc_start: 0.7462 (mm110) cc_final: 0.6958 (pm20) REVERT: W 131 ASP cc_start: 0.7209 (t70) cc_final: 0.6760 (t70) REVERT: X 86 GLN cc_start: 0.7456 (mm110) cc_final: 0.6957 (pm20) REVERT: Y 86 GLN cc_start: 0.7470 (mm110) cc_final: 0.6983 (pm20) REVERT: e 86 GLN cc_start: 0.7466 (mm110) cc_final: 0.6964 (pm20) outliers start: 1 outliers final: 0 residues processed: 589 average time/residue: 1.9299 time to fit residues: 1313.1077 Evaluate side-chains 537 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 8.9990 chunk 400 optimal weight: 0.8980 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 297 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 2 109 ASN 2 125 ASN 4 109 ASN 4 125 ASN 6 109 ASN 6 125 ASN 6 139 ASN A 109 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 60 HIS H 109 ASN H 125 ASN I 109 ASN I 125 ASN K 109 ASN K 125 ASN M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN P 109 ASN P 125 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 109 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN Y 60 HIS 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: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34776 Z= 0.229 Angle : 0.642 6.515 46848 Z= 0.338 Chirality : 0.041 0.144 4920 Planarity : 0.004 0.032 6192 Dihedral : 4.408 18.407 4536 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.16 % Allowed : 3.16 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.28 (0.13), residues: 4032 helix: 3.14 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.34 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP U 93 HIS 0.008 0.002 HIS I 128 PHE 0.016 0.003 PHE I 41 TYR 0.040 0.004 TYR A 32 ARG 0.004 0.001 ARG 2 22 *********************** 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 586 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 580 time to evaluate : 3.864 Fit side-chains REVERT: 4 86 GLN cc_start: 0.7451 (mm110) cc_final: 0.6930 (pm20) REVERT: 6 86 GLN cc_start: 0.7459 (mm110) cc_final: 0.6953 (pm20) REVERT: A 86 GLN cc_start: 0.7451 (mm110) cc_final: 0.6936 (pm20) REVERT: B 86 GLN cc_start: 0.7461 (mm110) cc_final: 0.6915 (pm20) REVERT: I 86 GLN cc_start: 0.7448 (mm110) cc_final: 0.6931 (pm20) REVERT: K 86 GLN cc_start: 0.7448 (mm110) cc_final: 0.6922 (pm20) REVERT: Q 86 GLN cc_start: 0.7459 (mm110) cc_final: 0.6946 (pm20) REVERT: S 86 GLN cc_start: 0.7460 (mm110) cc_final: 0.6939 (pm20) REVERT: W 86 GLN cc_start: 0.7447 (mm110) cc_final: 0.6937 (pm20) REVERT: a 86 GLN cc_start: 0.7453 (mm110) cc_final: 0.6937 (pm20) REVERT: r 86 GLN cc_start: 0.7448 (mm110) cc_final: 0.6935 (pm20) outliers start: 6 outliers final: 0 residues processed: 580 average time/residue: 1.9976 time to fit residues: 1330.3263 Evaluate side-chains 536 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 4.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 125 ASN 1 139 ASN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 6 109 ASN 6 125 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 F 109 ASN F 125 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 P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 109 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 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 r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34776 Z= 0.171 Angle : 0.558 6.071 46848 Z= 0.296 Chirality : 0.037 0.138 4920 Planarity : 0.003 0.022 6192 Dihedral : 4.305 18.151 4536 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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: 4.41 (0.13), residues: 4032 helix: 3.25 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.30 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP U 93 HIS 0.006 0.001 HIS E 128 PHE 0.014 0.002 PHE F 41 TYR 0.024 0.003 TYR A 32 ARG 0.003 0.001 ARG A 22 *********************** 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 572 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 572 time to evaluate : 3.945 Fit side-chains REVERT: 1 86 GLN cc_start: 0.7439 (mm110) cc_final: 0.6899 (pm20) REVERT: 4 86 GLN cc_start: 0.7454 (mm110) cc_final: 0.6926 (pm20) REVERT: 6 86 GLN cc_start: 0.7458 (mm110) cc_final: 0.6935 (pm20) REVERT: A 86 GLN cc_start: 0.7448 (mm110) cc_final: 0.6921 (pm20) REVERT: G 86 GLN cc_start: 0.7469 (mm110) cc_final: 0.6880 (pm20) REVERT: I 86 GLN cc_start: 0.7450 (mm110) cc_final: 0.6914 (pm20) REVERT: K 86 GLN cc_start: 0.7449 (mm110) cc_final: 0.6914 (pm20) REVERT: P 86 GLN cc_start: 0.7467 (mm110) cc_final: 0.6888 (pm20) REVERT: Q 86 GLN cc_start: 0.7458 (mm110) cc_final: 0.6930 (pm20) REVERT: W 86 GLN cc_start: 0.7450 (mm110) cc_final: 0.6917 (pm20) REVERT: Y 86 GLN cc_start: 0.7468 (mm110) cc_final: 0.6945 (pm20) REVERT: a 86 GLN cc_start: 0.7453 (mm110) cc_final: 0.6922 (pm20) REVERT: r 86 GLN cc_start: 0.7449 (mm110) cc_final: 0.6925 (pm20) outliers start: 0 outliers final: 0 residues processed: 572 average time/residue: 2.0305 time to fit residues: 1333.7056 Evaluate side-chains 551 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 336 optimal weight: 5.9990 chunk 272 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- 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 6 125 ASN 6 139 ASN A 109 ASN A 125 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 I 109 ASN I 125 ASN ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1105 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= 0.194 Angle : 0.587 6.292 46848 Z= 0.312 Chirality : 0.038 0.141 4920 Planarity : 0.004 0.027 6192 Dihedral : 4.358 18.091 4536 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.30 % Allowed : 4.74 % Favored : 94.96 % 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: 4.24 (0.13), residues: 4032 helix: 3.13 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.21 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 93 HIS 0.006 0.001 HIS F 128 PHE 0.014 0.003 PHE 6 41 TYR 0.022 0.003 TYR A 32 ARG 0.003 0.001 ARG A 22 *********************** 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 591 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 580 time to evaluate : 4.219 Fit side-chains REVERT: 1 86 GLN cc_start: 0.7440 (mm110) cc_final: 0.6858 (pm20) REVERT: 4 86 GLN cc_start: 0.7452 (mm110) cc_final: 0.6871 (pm20) REVERT: 6 86 GLN cc_start: 0.7461 (mm110) cc_final: 0.6932 (pm20) REVERT: A 86 GLN cc_start: 0.7447 (mm110) cc_final: 0.6872 (pm20) REVERT: G 60 HIS cc_start: 0.7999 (m-70) cc_final: 0.7798 (m170) REVERT: I 86 GLN cc_start: 0.7459 (mm110) cc_final: 0.6884 (pm20) REVERT: K 86 GLN cc_start: 0.7451 (mm110) cc_final: 0.6906 (pm20) REVERT: Q 86 GLN cc_start: 0.7459 (mm110) cc_final: 0.6882 (pm20) REVERT: S 86 GLN cc_start: 0.7466 (mm110) cc_final: 0.6918 (pm20) REVERT: W 86 GLN cc_start: 0.7463 (mm110) cc_final: 0.6897 (pm20) REVERT: Y 86 GLN cc_start: 0.7469 (mm110) cc_final: 0.6930 (pm20) REVERT: a 86 GLN cc_start: 0.7454 (mm110) cc_final: 0.6880 (pm20) REVERT: r 86 GLN cc_start: 0.7446 (mm110) cc_final: 0.6876 (pm20) outliers start: 11 outliers final: 0 residues processed: 580 average time/residue: 2.0552 time to fit residues: 1368.1647 Evaluate side-chains 554 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 8.9990 chunk 355 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 32 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 2 60 HIS 2 109 ASN 2 125 ASN 4 109 ASN 4 125 ASN 6 109 ASN 6 125 ASN 6 139 ASN A 60 HIS A 109 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 109 ASN I 125 ASN K 109 ASN K 125 ASN M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN P 60 HIS P 109 ASN P 125 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 109 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN X 109 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: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34776 Z= 0.216 Angle : 0.617 6.405 46848 Z= 0.328 Chirality : 0.039 0.142 4920 Planarity : 0.004 0.028 6192 Dihedral : 4.390 17.593 4536 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.14 % Allowed : 5.04 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.13), residues: 4032 helix: 3.06 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.14 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP 1 93 HIS 0.007 0.001 HIS I 128 PHE 0.015 0.003 PHE F 41 TYR 0.021 0.003 TYR a 39 ARG 0.004 0.001 ARG B 22 *********************** 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 623 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 581 time to evaluate : 4.184 Fit side-chains REVERT: 1 49 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6887 (ptpt) REVERT: 1 86 GLN cc_start: 0.7436 (mm110) cc_final: 0.6862 (pm20) REVERT: 2 49 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6895 (ptpt) REVERT: 2 86 GLN cc_start: 0.7469 (mm110) cc_final: 0.6923 (pm20) REVERT: 4 49 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6891 (ptpt) REVERT: 4 86 GLN cc_start: 0.7463 (mm110) cc_final: 0.6896 (pm20) REVERT: 6 49 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6874 (ptpt) REVERT: 6 86 GLN cc_start: 0.7455 (mm110) cc_final: 0.6879 (pm20) REVERT: A 49 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6888 (ptpt) REVERT: A 86 GLN cc_start: 0.7442 (mm110) cc_final: 0.6860 (pm20) REVERT: B 49 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6890 (ptpt) REVERT: B 86 GLN cc_start: 0.7462 (mm110) cc_final: 0.6912 (pm20) REVERT: E 49 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6873 (ptpt) REVERT: E 86 GLN cc_start: 0.7470 (mm110) cc_final: 0.6910 (pm20) REVERT: F 49 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6888 (ptpt) REVERT: F 86 GLN cc_start: 0.7474 (mm110) cc_final: 0.6927 (pm20) REVERT: G 49 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6891 (ptpt) REVERT: G 86 GLN cc_start: 0.7481 (mm110) cc_final: 0.6886 (pm20) REVERT: H 49 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6883 (ptpt) REVERT: I 49 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6893 (ptpt) REVERT: I 86 GLN cc_start: 0.7454 (mm110) cc_final: 0.6882 (pm20) REVERT: K 49 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6887 (ptpt) REVERT: K 86 GLN cc_start: 0.7442 (mm110) cc_final: 0.6860 (pm20) REVERT: O 49 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6880 (ptpt) REVERT: O 86 GLN cc_start: 0.7470 (mm110) cc_final: 0.6919 (pm20) REVERT: P 49 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6886 (ptpt) REVERT: Q 49 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6890 (ptpt) REVERT: Q 86 GLN cc_start: 0.7455 (mm110) cc_final: 0.6876 (pm20) REVERT: S 49 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: S 86 GLN cc_start: 0.7470 (mm110) cc_final: 0.6928 (pm20) REVERT: U 49 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6879 (ptpt) REVERT: U 86 GLN cc_start: 0.7470 (mm110) cc_final: 0.6914 (pm20) REVERT: W 49 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6891 (ptpt) REVERT: W 86 GLN cc_start: 0.7461 (mm110) cc_final: 0.6902 (pm20) REVERT: X 49 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: X 86 GLN cc_start: 0.7463 (mm110) cc_final: 0.6907 (pm20) REVERT: Y 49 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6888 (ptpt) REVERT: Y 86 GLN cc_start: 0.7474 (mm110) cc_final: 0.6935 (pm20) REVERT: a 49 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6886 (ptpt) REVERT: a 86 GLN cc_start: 0.7450 (mm110) cc_final: 0.6878 (pm20) REVERT: e 49 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6899 (ptpt) REVERT: e 86 GLN cc_start: 0.7469 (mm110) cc_final: 0.6924 (pm20) REVERT: r 49 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6886 (ptpt) REVERT: r 86 GLN cc_start: 0.7445 (mm110) cc_final: 0.6877 (pm20) outliers start: 42 outliers final: 0 residues processed: 581 average time/residue: 2.0702 time to fit residues: 1376.6308 Evaluate side-chains 599 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 576 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 49 LYS Chi-restraints excluded: chain 4 residue 49 LYS Chi-restraints excluded: chain 6 residue 49 LYS Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain Q residue 49 LYS Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 49 LYS Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain a residue 49 LYS Chi-restraints excluded: chain e residue 49 LYS Chi-restraints excluded: chain r residue 49 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 4 109 ASN 4 125 ASN 6 109 ASN 6 125 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 G 60 HIS G 109 ASN G 125 ASN G 139 ASN H 109 ASN H 125 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 Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 109 ASN U 125 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 Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.003 0.021 34776 Z= 0.193 Angle : 0.582 6.268 46848 Z= 0.311 Chirality : 0.038 0.137 4920 Planarity : 0.003 0.026 6192 Dihedral : 4.363 18.045 4536 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.65 % Allowed : 5.72 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.13), residues: 4032 helix: 3.16 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.24 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 93 HIS 0.006 0.001 HIS I 128 PHE 0.014 0.003 PHE F 41 TYR 0.019 0.003 TYR I 39 ARG 0.003 0.001 ARG P 22 *********************** 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 640 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 616 time to evaluate : 4.240 Fit side-chains REVERT: 1 49 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: 1 86 GLN cc_start: 0.7433 (mm110) cc_final: 0.6849 (pm20) REVERT: 2 49 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6875 (ptpt) REVERT: 2 86 GLN cc_start: 0.7466 (mm110) cc_final: 0.6915 (pm20) REVERT: 4 49 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6875 (ptpt) REVERT: 4 86 GLN cc_start: 0.7452 (mm110) cc_final: 0.6866 (pm20) REVERT: 6 49 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6859 (ptpt) REVERT: 6 86 GLN cc_start: 0.7451 (mm110) cc_final: 0.6871 (pm20) REVERT: A 49 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6880 (ptpt) REVERT: A 86 GLN cc_start: 0.7436 (mm110) cc_final: 0.6853 (pm20) REVERT: B 49 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6887 (ptpt) REVERT: B 86 GLN cc_start: 0.7465 (mm110) cc_final: 0.6903 (pm20) REVERT: E 49 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6852 (ptpt) REVERT: E 86 GLN cc_start: 0.7457 (mm110) cc_final: 0.6902 (pm20) REVERT: F 49 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6875 (ptpt) REVERT: F 86 GLN cc_start: 0.7472 (mm110) cc_final: 0.6918 (pm20) REVERT: G 49 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: G 86 GLN cc_start: 0.7477 (mm110) cc_final: 0.6881 (pm20) REVERT: H 49 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: H 86 GLN cc_start: 0.7480 (mm110) cc_final: 0.6882 (pm20) REVERT: I 49 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: I 86 GLN cc_start: 0.7441 (mm110) cc_final: 0.6850 (pm20) REVERT: K 49 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6874 (ptpt) REVERT: K 86 GLN cc_start: 0.7441 (mm110) cc_final: 0.6849 (pm20) REVERT: M 49 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6896 (ptpt) REVERT: M 86 GLN cc_start: 0.7466 (mm110) cc_final: 0.6917 (pm20) REVERT: O 49 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6862 (ptpt) REVERT: O 86 GLN cc_start: 0.7469 (mm110) cc_final: 0.6909 (pm20) REVERT: P 49 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6875 (ptpt) REVERT: P 86 GLN cc_start: 0.7473 (mm110) cc_final: 0.6874 (pm20) REVERT: Q 49 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6873 (ptpt) REVERT: Q 86 GLN cc_start: 0.7450 (mm110) cc_final: 0.6868 (pm20) REVERT: S 49 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6862 (ptpt) REVERT: S 86 GLN cc_start: 0.7456 (mm110) cc_final: 0.6921 (pm20) REVERT: U 49 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6864 (ptpt) REVERT: U 86 GLN cc_start: 0.7456 (mm110) cc_final: 0.6906 (pm20) REVERT: W 49 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6873 (ptpt) REVERT: W 86 GLN cc_start: 0.7447 (mm110) cc_final: 0.6863 (pm20) REVERT: X 49 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6862 (ptpt) REVERT: X 86 GLN cc_start: 0.7447 (mm110) cc_final: 0.6900 (pm20) REVERT: Y 49 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6879 (ptpt) REVERT: Y 86 GLN cc_start: 0.7470 (mm110) cc_final: 0.6925 (pm20) REVERT: a 49 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6869 (ptpt) REVERT: a 86 GLN cc_start: 0.7446 (mm110) cc_final: 0.6868 (pm20) REVERT: e 49 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6877 (ptpt) REVERT: e 86 GLN cc_start: 0.7470 (mm110) cc_final: 0.6915 (pm20) REVERT: r 49 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6877 (ptpt) REVERT: r 86 GLN cc_start: 0.7438 (mm110) cc_final: 0.6862 (pm20) outliers start: 24 outliers final: 0 residues processed: 616 average time/residue: 2.0692 time to fit residues: 1458.5460 Evaluate side-chains 589 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 565 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 49 LYS Chi-restraints excluded: chain 4 residue 49 LYS Chi-restraints excluded: chain 6 residue 49 LYS Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain Q residue 49 LYS Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 49 LYS Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain a residue 49 LYS Chi-restraints excluded: chain e residue 49 LYS Chi-restraints excluded: chain r residue 49 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 2 109 ASN 2 125 ASN 4 109 ASN 4 125 ASN 6 109 ASN 6 125 ASN 6 139 ASN A 109 ASN A 125 ASN B 109 ASN B 125 ASN B 139 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 109 ASN I 125 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 P 109 ASN P 125 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 109 ASN U 125 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 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: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 34776 Z= 0.161 Angle : 0.537 5.994 46848 Z= 0.288 Chirality : 0.036 0.134 4920 Planarity : 0.003 0.019 6192 Dihedral : 4.295 18.150 4536 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.63 % Allowed : 6.18 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.51 (0.13), residues: 4032 helix: 3.31 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.34 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP I 93 HIS 0.005 0.001 HIS I 128 PHE 0.012 0.002 PHE F 41 TYR 0.017 0.002 TYR A 39 ARG 0.002 0.001 ARG P 22 *********************** 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 622 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 599 time to evaluate : 4.398 Fit side-chains REVERT: 1 49 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6870 (ptpt) REVERT: 1 86 GLN cc_start: 0.7427 (mm110) cc_final: 0.6837 (pm20) REVERT: 2 49 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6875 (ptpt) REVERT: 2 86 GLN cc_start: 0.7448 (mm110) cc_final: 0.6906 (pm20) REVERT: 4 49 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6869 (ptpt) REVERT: 4 86 GLN cc_start: 0.7444 (mm110) cc_final: 0.6856 (pm20) REVERT: 6 49 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6856 (ptpt) REVERT: 6 86 GLN cc_start: 0.7443 (mm110) cc_final: 0.6862 (pm20) REVERT: A 49 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6872 (ptpt) REVERT: A 86 GLN cc_start: 0.7428 (mm110) cc_final: 0.6845 (pm20) REVERT: B 86 GLN cc_start: 0.7447 (mm110) cc_final: 0.6891 (pm20) REVERT: E 49 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6848 (ptpt) REVERT: E 86 GLN cc_start: 0.7446 (mm110) cc_final: 0.6892 (pm20) REVERT: F 49 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6860 (ptpt) REVERT: F 86 GLN cc_start: 0.7452 (mm110) cc_final: 0.6909 (pm20) REVERT: G 49 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6870 (ptpt) REVERT: G 86 GLN cc_start: 0.7468 (mm110) cc_final: 0.6867 (pm20) REVERT: H 49 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6867 (ptpt) REVERT: H 86 GLN cc_start: 0.7467 (mm110) cc_final: 0.6867 (pm20) REVERT: I 49 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6872 (ptpt) REVERT: I 86 GLN cc_start: 0.7449 (mm110) cc_final: 0.6866 (pm20) REVERT: K 49 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6869 (ptpt) REVERT: K 86 GLN cc_start: 0.7448 (mm110) cc_final: 0.6862 (pm20) REVERT: M 49 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6877 (ptpt) REVERT: M 86 GLN cc_start: 0.7451 (mm110) cc_final: 0.6909 (pm20) REVERT: O 49 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6855 (ptpt) REVERT: O 86 GLN cc_start: 0.7450 (mm110) cc_final: 0.6897 (pm20) REVERT: P 49 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6870 (ptpt) REVERT: P 86 GLN cc_start: 0.7459 (mm110) cc_final: 0.6868 (pm20) REVERT: Q 49 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6857 (ptpt) REVERT: Q 86 GLN cc_start: 0.7444 (mm110) cc_final: 0.6859 (pm20) REVERT: S 49 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6858 (ptpt) REVERT: S 86 GLN cc_start: 0.7459 (mm110) cc_final: 0.6914 (pm20) REVERT: U 49 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6858 (ptpt) REVERT: U 86 GLN cc_start: 0.7446 (mm110) cc_final: 0.6896 (pm20) REVERT: W 49 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6868 (ptpt) REVERT: W 86 GLN cc_start: 0.7439 (mm110) cc_final: 0.6854 (pm20) REVERT: X 49 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6855 (ptpt) REVERT: X 86 GLN cc_start: 0.7440 (mm110) cc_final: 0.6890 (pm20) REVERT: Y 49 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6871 (ptpt) REVERT: Y 86 GLN cc_start: 0.7450 (mm110) cc_final: 0.6918 (pm20) REVERT: a 49 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6865 (ptpt) REVERT: a 86 GLN cc_start: 0.7443 (mm110) cc_final: 0.6858 (pm20) REVERT: e 49 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6872 (ptpt) REVERT: e 86 GLN cc_start: 0.7449 (mm110) cc_final: 0.6903 (pm20) REVERT: r 49 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6870 (ptpt) REVERT: r 86 GLN cc_start: 0.7446 (mm110) cc_final: 0.6871 (pm20) outliers start: 23 outliers final: 0 residues processed: 599 average time/residue: 2.0958 time to fit residues: 1434.9798 Evaluate side-chains 612 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 589 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 49 LYS Chi-restraints excluded: chain 4 residue 49 LYS Chi-restraints excluded: chain 6 residue 49 LYS Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain Q residue 49 LYS Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 49 LYS Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain a residue 49 LYS Chi-restraints excluded: chain e residue 49 LYS Chi-restraints excluded: chain r residue 49 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 9.9990 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 331 optimal weight: 0.9990 chunk 346 optimal weight: 0.9980 chunk 365 optimal weight: 6.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 2 109 ASN 2 125 ASN 4 109 ASN 4 125 ASN 6 109 ASN 6 125 ASN 6 139 ASN A 109 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 109 ASN I 125 ASN K 109 ASN K 125 ASN M 109 ASN M 125 ASN M 139 ASN O 109 ASN O 125 ASN P 109 ASN P 125 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 109 ASN U 125 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 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: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 34776 Z= 0.125 Angle : 0.475 5.640 46848 Z= 0.255 Chirality : 0.035 0.129 4920 Planarity : 0.002 0.014 6192 Dihedral : 4.144 19.057 4536 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.57 % Allowed : 6.45 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.87 (0.13), residues: 4032 helix: 3.59 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.35 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 93 HIS 0.004 0.001 HIS K 128 PHE 0.010 0.002 PHE e 41 TYR 0.015 0.002 TYR e 39 ARG 0.001 0.000 ARG G 76 *********************** 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 618 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 597 time to evaluate : 3.950 Fit side-chains REVERT: 1 49 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6851 (ptpt) REVERT: 1 86 GLN cc_start: 0.7424 (mm110) cc_final: 0.6833 (pm20) REVERT: 2 49 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6854 (ptpt) REVERT: 2 86 GLN cc_start: 0.7447 (mm110) cc_final: 0.6903 (pm20) REVERT: 4 49 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6852 (ptpt) REVERT: 4 86 GLN cc_start: 0.7439 (mm110) cc_final: 0.6846 (pm20) REVERT: 6 49 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6831 (ptpt) REVERT: 6 86 GLN cc_start: 0.7439 (mm110) cc_final: 0.6852 (pm20) REVERT: A 49 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6856 (ptpt) REVERT: A 86 GLN cc_start: 0.7431 (mm110) cc_final: 0.6839 (pm20) REVERT: B 86 GLN cc_start: 0.7444 (mm110) cc_final: 0.6894 (pm20) REVERT: E 49 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6828 (ptpt) REVERT: E 86 GLN cc_start: 0.7441 (mm110) cc_final: 0.6885 (pm20) REVERT: F 49 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6842 (ptpt) REVERT: F 86 GLN cc_start: 0.7452 (mm110) cc_final: 0.6910 (pm20) REVERT: G 49 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6852 (ptpt) REVERT: G 86 GLN cc_start: 0.7454 (mm110) cc_final: 0.6844 (pm20) REVERT: H 49 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6848 (ptpt) REVERT: H 86 GLN cc_start: 0.7460 (mm110) cc_final: 0.6853 (pm20) REVERT: I 49 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6852 (ptpt) REVERT: I 86 GLN cc_start: 0.7447 (mm110) cc_final: 0.6856 (pm20) REVERT: K 49 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6850 (ptpt) REVERT: K 86 GLN cc_start: 0.7441 (mm110) cc_final: 0.6848 (pm20) REVERT: M 49 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6858 (ptpt) REVERT: M 86 GLN cc_start: 0.7448 (mm110) cc_final: 0.6906 (pm20) REVERT: O 49 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6835 (ptpt) REVERT: O 86 GLN cc_start: 0.7461 (mm110) cc_final: 0.6909 (pm20) REVERT: P 49 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6853 (ptpt) REVERT: P 86 GLN cc_start: 0.7449 (mm110) cc_final: 0.6854 (pm20) REVERT: Q 86 GLN cc_start: 0.7442 (mm110) cc_final: 0.6850 (pm20) REVERT: S 49 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6840 (ptpt) REVERT: S 86 GLN cc_start: 0.7445 (mm110) cc_final: 0.6902 (pm20) REVERT: U 49 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6838 (ptpt) REVERT: U 86 GLN cc_start: 0.7440 (mm110) cc_final: 0.6891 (pm20) REVERT: W 49 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6851 (ptpt) REVERT: W 86 GLN cc_start: 0.7436 (mm110) cc_final: 0.6847 (pm20) REVERT: X 49 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6834 (ptpt) REVERT: X 86 GLN cc_start: 0.7439 (mm110) cc_final: 0.6890 (pm20) REVERT: Y 49 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6852 (ptpt) REVERT: Y 86 GLN cc_start: 0.7443 (mm110) cc_final: 0.6906 (pm20) REVERT: a 49 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6846 (ptpt) REVERT: a 86 GLN cc_start: 0.7440 (mm110) cc_final: 0.6849 (pm20) REVERT: e 86 GLN cc_start: 0.7434 (mm110) cc_final: 0.6888 (pm20) REVERT: r 49 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6849 (ptpt) REVERT: r 86 GLN cc_start: 0.7435 (mm110) cc_final: 0.6849 (pm20) outliers start: 21 outliers final: 0 residues processed: 597 average time/residue: 2.0816 time to fit residues: 1419.4918 Evaluate side-chains 608 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 587 time to evaluate : 4.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 49 LYS Chi-restraints excluded: chain 4 residue 49 LYS Chi-restraints excluded: chain 6 residue 49 LYS Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 49 LYS Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain a residue 49 LYS Chi-restraints excluded: chain r residue 49 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 269 optimal weight: 0.9990 chunk 406 optimal weight: 5.9990 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 4 109 ASN 6 109 ASN 6 125 ASN 6 139 ASN A 109 ASN A 125 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 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 P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 109 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN X 125 ASN X 139 ASN Y 109 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34776 Z= 0.166 Angle : 0.542 6.056 46848 Z= 0.290 Chirality : 0.037 0.131 4920 Planarity : 0.003 0.018 6192 Dihedral : 4.276 19.623 4536 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.60 % Allowed : 6.45 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.13), residues: 4032 helix: 3.40 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.36 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 93 HIS 0.005 0.001 HIS O 128 PHE 0.012 0.002 PHE F 41 TYR 0.018 0.002 TYR I 39 ARG 0.002 0.001 ARG S 22 ********************** 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 618 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 596 time to evaluate : 4.123 Fit side-chains REVERT: 1 49 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: 1 86 GLN cc_start: 0.7436 (mm110) cc_final: 0.6848 (pm20) REVERT: 2 49 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6877 (ptpt) REVERT: 2 86 GLN cc_start: 0.7457 (mm110) cc_final: 0.6905 (pm20) REVERT: 4 49 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6877 (ptpt) REVERT: 4 86 GLN cc_start: 0.7449 (mm110) cc_final: 0.6866 (pm20) REVERT: 6 49 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6860 (ptpt) REVERT: 6 86 GLN cc_start: 0.7449 (mm110) cc_final: 0.6872 (pm20) REVERT: A 49 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6878 (ptpt) REVERT: A 86 GLN cc_start: 0.7439 (mm110) cc_final: 0.6854 (pm20) REVERT: B 49 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: B 86 GLN cc_start: 0.7456 (mm110) cc_final: 0.6894 (pm20) REVERT: E 49 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6854 (ptpt) REVERT: E 86 GLN cc_start: 0.7460 (mm110) cc_final: 0.6896 (pm20) REVERT: F 49 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6868 (ptpt) REVERT: F 86 GLN cc_start: 0.7465 (mm110) cc_final: 0.6914 (pm20) REVERT: G 49 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6877 (ptpt) REVERT: G 86 GLN cc_start: 0.7462 (mm110) cc_final: 0.6866 (pm20) REVERT: H 49 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6875 (ptpt) REVERT: H 86 GLN cc_start: 0.7467 (mm110) cc_final: 0.6871 (pm20) REVERT: I 49 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: I 86 GLN cc_start: 0.7443 (mm110) cc_final: 0.6850 (pm20) REVERT: K 49 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6874 (ptpt) REVERT: K 86 GLN cc_start: 0.7442 (mm110) cc_final: 0.6846 (pm20) REVERT: M 49 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6884 (ptpt) REVERT: M 86 GLN cc_start: 0.7458 (mm110) cc_final: 0.6907 (pm20) REVERT: O 49 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6863 (ptpt) REVERT: O 86 GLN cc_start: 0.7457 (mm110) cc_final: 0.6896 (pm20) REVERT: P 49 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6876 (ptpt) REVERT: P 86 GLN cc_start: 0.7463 (mm110) cc_final: 0.6867 (pm20) REVERT: Q 86 GLN cc_start: 0.7449 (mm110) cc_final: 0.6866 (pm20) REVERT: S 49 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6867 (ptpt) REVERT: S 86 GLN cc_start: 0.7463 (mm110) cc_final: 0.6921 (pm20) REVERT: U 49 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6864 (ptpt) REVERT: U 86 GLN cc_start: 0.7462 (mm110) cc_final: 0.6903 (pm20) REVERT: W 49 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6874 (ptpt) REVERT: W 86 GLN cc_start: 0.7445 (mm110) cc_final: 0.6865 (pm20) REVERT: X 49 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6858 (ptpt) REVERT: X 86 GLN cc_start: 0.7455 (mm110) cc_final: 0.6900 (pm20) REVERT: Y 49 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6878 (ptpt) REVERT: Y 86 GLN cc_start: 0.7461 (mm110) cc_final: 0.6922 (pm20) REVERT: a 49 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6873 (ptpt) REVERT: a 86 GLN cc_start: 0.7446 (mm110) cc_final: 0.6866 (pm20) REVERT: e 86 GLN cc_start: 0.7463 (mm110) cc_final: 0.6909 (pm20) REVERT: r 49 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6877 (ptpt) REVERT: r 86 GLN cc_start: 0.7441 (mm110) cc_final: 0.6864 (pm20) outliers start: 22 outliers final: 0 residues processed: 596 average time/residue: 2.0853 time to fit residues: 1421.6947 Evaluate side-chains 603 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 581 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 49 LYS Chi-restraints excluded: chain 4 residue 49 LYS Chi-restraints excluded: chain 6 residue 49 LYS Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain X residue 49 LYS Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain a residue 49 LYS Chi-restraints excluded: chain r residue 49 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 332 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 4 109 ASN 4 125 ASN 6 109 ASN 6 125 ASN 6 139 ASN A 109 ASN A 125 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 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 P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 109 ASN U 125 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 a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 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 = 0.3579 r_free = 0.3579 target = 0.163484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.155631 restraints weight = 19939.108| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.33 r_work: 0.3388 rms_B_bonded: 0.61 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.3026 rms_B_bonded: 3.46 restraints_weight: 0.1250 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1274 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= 0.183 Angle : 0.567 6.162 46848 Z= 0.304 Chirality : 0.038 0.133 4920 Planarity : 0.003 0.022 6192 Dihedral : 4.308 19.149 4536 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.63 % Allowed : 6.45 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.49 (0.13), residues: 4032 helix: 3.31 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.31 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP O 93 HIS 0.006 0.001 HIS O 128 PHE 0.013 0.002 PHE F 41 TYR 0.019 0.002 TYR M 39 ARG 0.003 0.001 ARG 1 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18897.89 seconds wall clock time: 334 minutes 38.43 seconds (20078.43 seconds total)