Starting phenix.real_space_refine on Sat Dec 16 18:12:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/12_2023/8cpm_16783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/12_2023/8cpm_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_16783/12_2023/8cpm_16783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/12_2023/8cpm_16783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/12_2023/8cpm_16783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpm_16783/12_2023/8cpm_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-1.21rc1-5172/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: 19.32, per 1000 atoms: 0.54 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: 18.12 Conformation dependent library (CDL) restraints added in 6.1 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: 5.62 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: 11.28 Time building geometry restraints manager: 18.84 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.030 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 97.260 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.380 ------------------------------------------------------------------------------- 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 : 4.812 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 1.9405 time to fit residues: 1385.1153 Evaluate side-chains 562 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 4.825 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4384 ------------------------------------------------------------------------------- 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 : 4.204 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 589 average time/residue: 1.9925 time to fit residues: 1360.2795 Evaluate side-chains 545 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 4.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7972 ------------------------------------------------------------------------------- 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 86 GLN 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 86 GLN B 109 ASN B 125 ASN E 86 GLN E 109 ASN E 125 ASN F 86 GLN 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 86 GLN M 109 ASN M 125 ASN M 139 ASN O 86 GLN O 109 ASN O 125 ASN P 109 ASN P 125 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 86 GLN S 109 ASN S 125 ASN U 109 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN X 86 GLN 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 86 GLN e 109 ASN e 125 ASN r 109 ASN r 125 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1056 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= 0.231 Angle : 0.643 6.492 46848 Z= 0.339 Chirality : 0.040 0.144 4920 Planarity : 0.004 0.033 6192 Dihedral : 4.413 18.448 4536 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.33 % Allowed : 3.40 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.26 (0.13), residues: 4032 helix: 3.13 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.29 (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 0.041 0.004 TYR A 32 ARG 0.004 0.001 ARG 4 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 620 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 608 time to evaluate : 4.547 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 608 average time/residue: 2.1163 time to fit residues: 1480.8576 Evaluate side-chains 555 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 555 time to evaluate : 4.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2258 ------------------------------------------------------------------------------- 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: 0.5980 chunk 279 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 109 ASN 1 125 ASN 1 139 ASN 2 86 GLN 2 109 ASN 2 125 ASN 2 139 ASN 4 86 GLN 4 109 ASN 4 125 ASN 6 109 ASN 6 125 ASN 6 139 ASN A 86 GLN A 109 ASN A 125 ASN A 139 ASN B 109 ASN B 125 ASN B 139 ASN E 86 GLN E 109 ASN E 125 ASN F 86 GLN 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 86 GLN I 109 ASN I 125 ASN I 139 ASN K 86 GLN K 109 ASN K 125 ASN K 139 ASN M 86 GLN M 109 ASN M 125 ASN M 139 ASN O 86 GLN O 109 ASN O 125 ASN P 109 ASN P 125 ASN P 139 ASN Q 86 GLN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 86 GLN U 109 ASN U 125 ASN W 86 GLN W 109 ASN W 125 ASN W 139 ASN X 86 GLN X 109 ASN X 125 ASN Y 86 GLN Y 109 ASN Y 125 ASN Y 139 ASN a 86 GLN a 109 ASN a 125 ASN a 139 ASN e 86 GLN e 109 ASN e 125 ASN r 86 GLN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 34776 Z= 0.160 Angle : 0.538 5.991 46848 Z= 0.286 Chirality : 0.036 0.140 4920 Planarity : 0.003 0.019 6192 Dihedral : 4.253 18.110 4536 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.49 % Allowed : 5.15 % Favored : 94.36 % 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: 3.34 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.24 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP M 93 HIS 0.006 0.001 HIS F 128 PHE 0.014 0.002 PHE I 41 TYR 0.022 0.003 TYR A 32 ARG 0.002 0.001 ARG M 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 629 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 611 time to evaluate : 4.664 Fit side-chains outliers start: 18 outliers final: 1 residues processed: 611 average time/residue: 2.0951 time to fit residues: 1471.2972 Evaluate side-chains 589 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 588 time to evaluate : 4.316 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.7386 time to fit residues: 7.7160 ------------------------------------------------------------------------------- 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: 6.9990 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 272 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 0.9980 chunk 353 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 125 ASN 1 139 ASN 2 86 GLN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 86 GLN E 109 ASN E 125 ASN E 139 ASN F 86 GLN F 109 ASN F 125 ASN F 139 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 125 ASN G 139 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 86 GLN M 109 ASN M 125 ASN M 139 ASN O 86 GLN O 109 ASN O 125 ASN O 139 ASN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 86 GLN U 109 ASN U 125 ASN U 139 ASN W 109 ASN W 125 ASN W 139 ASN X 86 GLN 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 86 GLN e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN r 139 ASN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34776 Z= 0.204 Angle : 0.598 6.309 46848 Z= 0.318 Chirality : 0.039 0.143 4920 Planarity : 0.004 0.025 6192 Dihedral : 4.367 17.975 4536 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.65 % Allowed : 5.28 % Favored : 94.06 % 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: 4.21 (0.13), residues: 4032 helix: 3.13 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.13 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP r 93 HIS 0.007 0.001 HIS I 128 PHE 0.015 0.003 PHE I 41 TYR 0.021 0.003 TYR A 32 ARG 0.003 0.001 ARG X 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 646 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 622 time to evaluate : 4.478 Fit side-chains outliers start: 24 outliers final: 3 residues processed: 622 average time/residue: 2.1226 time to fit residues: 1517.9803 Evaluate side-chains 577 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 574 time to evaluate : 4.235 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.6823 time to fit residues: 11.5433 ------------------------------------------------------------------------------- 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: 0.7980 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 125 ASN 2 60 HIS 2 86 GLN 2 109 ASN 2 125 ASN 4 109 ASN 4 125 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 ASN 6 125 ASN 6 139 ASN A 60 HIS A 109 ASN A 125 ASN B 109 ASN B 125 ASN B 139 ASN E 86 GLN E 109 ASN E 125 ASN F 86 GLN F 109 ASN F 125 ASN G 60 HIS ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 125 ASN G 139 ASN H 60 HIS ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN H 125 ASN I 109 ASN I 125 ASN K 109 ASN K 125 ASN M 86 GLN M 109 ASN M 125 ASN M 139 ASN O 86 GLN O 109 ASN O 125 ASN P 60 HIS ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN P 125 ASN Q 109 ASN Q 125 ASN Q 139 ASN S 109 ASN S 125 ASN U 86 GLN U 109 ASN U 125 ASN W 109 ASN W 125 ASN W 139 ASN X 86 GLN X 109 ASN X 125 ASN Y 60 HIS Y 86 GLN Y 109 ASN Y 125 ASN a 109 ASN a 125 ASN a 139 ASN e 86 GLN e 109 ASN e 125 ASN r 109 ASN r 125 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34776 Z= 0.234 Angle : 0.638 6.480 46848 Z= 0.339 Chirality : 0.040 0.143 4920 Planarity : 0.004 0.029 6192 Dihedral : 4.408 17.375 4536 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.47 % Allowed : 5.56 % 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: 4.04 (0.13), residues: 4032 helix: 3.02 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.04 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP M 93 HIS 0.007 0.002 HIS I 128 PHE 0.015 0.003 PHE I 41 TYR 0.022 0.003 TYR e 39 ARG 0.004 0.001 ARG A 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 667 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 613 time to evaluate : 4.199 Fit side-chains outliers start: 54 outliers final: 8 residues processed: 613 average time/residue: 2.0704 time to fit residues: 1456.5000 Evaluate side-chains 570 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 562 time to evaluate : 4.049 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.6894 time to fit residues: 21.3562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 2 86 GLN 2 109 ASN 2 125 ASN 2 139 ASN 4 109 ASN 4 125 ASN 4 139 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 ASN 6 125 ASN 6 136 HIS 6 139 ASN A 109 ASN A 125 ASN B 109 ASN B 125 ASN B 139 ASN E 86 GLN E 109 ASN E 125 ASN E 139 ASN F 86 GLN F 109 ASN F 125 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 125 ASN G 136 HIS G 139 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN H 125 ASN H 139 ASN I 86 GLN 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 86 GLN M 109 ASN M 125 ASN M 139 ASN O 86 GLN O 109 ASN O 125 ASN O 139 ASN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN P 125 ASN P 139 ASN Q 109 ASN Q 125 ASN Q 136 HIS Q 139 ASN S 109 ASN S 125 ASN S 139 ASN U 86 GLN U 109 ASN U 125 ASN U 139 ASN W 109 ASN W 125 ASN W 136 HIS W 139 ASN X 86 GLN 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 86 GLN e 109 ASN e 125 ASN e 139 ASN r 109 ASN r 125 ASN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34776 Z= 0.248 Angle : 0.668 6.551 46848 Z= 0.352 Chirality : 0.040 0.145 4920 Planarity : 0.004 0.031 6192 Dihedral : 4.442 17.223 4536 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.35 % Allowed : 6.81 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.13), residues: 4032 helix: 2.95 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.04 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP K 93 HIS 0.008 0.002 HIS r 128 PHE 0.016 0.003 PHE W 41 TYR 0.021 0.003 TYR I 39 ARG 0.005 0.001 ARG 1 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 627 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 614 time to evaluate : 5.058 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 614 average time/residue: 2.1098 time to fit residues: 1489.1478 Evaluate side-chains 586 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 583 time to evaluate : 4.379 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.7962 time to fit residues: 12.4124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 267 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 139 ASN 2 86 GLN 2 109 ASN 2 139 ASN 4 109 ASN 4 125 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 ASN 6 139 ASN A 109 ASN B 109 ASN B 139 ASN E 86 GLN E 109 ASN F 86 GLN F 109 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 139 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN H 139 ASN I 109 ASN I 139 ASN K 109 ASN K 139 ASN M 86 GLN M 109 ASN M 139 ASN O 86 GLN O 109 ASN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN Q 109 ASN Q 139 ASN S 109 ASN U 86 GLN U 109 ASN W 109 ASN W 125 ASN W 139 ASN X 86 GLN X 109 ASN Y 109 ASN Y 139 ASN a 109 ASN a 125 ASN a 139 ASN e 86 GLN e 109 ASN e 125 ASN r 109 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34776 Z= 0.238 Angle : 0.650 6.522 46848 Z= 0.344 Chirality : 0.040 0.144 4920 Planarity : 0.004 0.029 6192 Dihedral : 4.465 17.440 4536 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.49 % Allowed : 6.54 % 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: 3.97 (0.13), residues: 4032 helix: 2.96 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.04 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP M 93 HIS 0.007 0.002 HIS I 128 PHE 0.015 0.003 PHE I 41 TYR 0.021 0.003 TYR U 39 ARG 0.004 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 627 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 609 time to evaluate : 4.768 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 609 average time/residue: 2.0987 time to fit residues: 1468.8722 Evaluate side-chains 588 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 579 time to evaluate : 4.205 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 1.8570 time to fit residues: 25.4778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 2.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 331 optimal weight: 0.9990 chunk 346 optimal weight: 0.9980 chunk 365 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 139 ASN 2 86 GLN 2 109 ASN 4 109 ASN 4 125 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 ASN 6 139 ASN A 109 ASN B 109 ASN B 139 ASN E 86 GLN E 109 ASN F 86 GLN F 109 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 139 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN I 109 ASN I 139 ASN K 109 ASN K 139 ASN M 86 GLN M 109 ASN M 139 ASN O 86 GLN O 109 ASN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN P 139 ASN Q 109 ASN Q 139 ASN S 109 ASN U 86 GLN U 109 ASN W 109 ASN W 125 ASN W 139 ASN X 86 GLN X 109 ASN Y 86 GLN Y 109 ASN a 109 ASN a 125 ASN a 139 ASN e 86 GLN e 109 ASN e 125 ASN r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1301 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= 0.179 Angle : 0.565 6.136 46848 Z= 0.302 Chirality : 0.037 0.137 4920 Planarity : 0.003 0.022 6192 Dihedral : 4.360 18.827 4536 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.49 % Allowed : 6.81 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.31 (0.13), residues: 4032 helix: 3.20 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.14 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP K 93 HIS 0.005 0.001 HIS r 128 PHE 0.013 0.002 PHE I 41 TYR 0.019 0.002 TYR S 39 ARG 0.003 0.001 ARG Y 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 583 time to evaluate : 4.428 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 583 average time/residue: 2.2846 time to fit residues: 1524.3310 Evaluate side-chains 577 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 567 time to evaluate : 4.444 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 1.8171 time to fit residues: 27.2772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.0970 chunk 374 optimal weight: 9.9990 chunk 323 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 250 optimal weight: 0.5980 chunk 198 optimal weight: 8.9990 overall best weight: 2.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 4 125 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 ASN 6 139 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 139 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN I 109 ASN K 109 ASN M 109 ASN M 139 ASN O 109 ASN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN Q 109 ASN Q 139 ASN S 86 GLN S 109 ASN U 109 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN Y 109 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN r 109 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1287 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= 0.183 Angle : 0.576 6.203 46848 Z= 0.308 Chirality : 0.038 0.136 4920 Planarity : 0.003 0.022 6192 Dihedral : 4.384 19.128 4536 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.08 % Allowed : 7.33 % Favored : 92.59 % 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: 4.31 (0.13), residues: 4032 helix: 3.21 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.12 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP U 93 HIS 0.006 0.001 HIS I 128 PHE 0.013 0.002 PHE M 41 TYR 0.019 0.003 TYR P 39 ARG 0.003 0.001 ARG a 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 576 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 573 time to evaluate : 4.765 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 573 average time/residue: 2.2564 time to fit residues: 1480.7585 Evaluate side-chains 562 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 4.210 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 2.9990 chunk 344 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 139 ASN 2 109 ASN 4 109 ASN 4 125 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 ASN 6 139 ASN A 109 ASN B 109 ASN B 139 ASN E 109 ASN F 109 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 139 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN I 109 ASN I 139 ASN K 109 ASN M 109 ASN M 139 ASN O 109 ASN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN Q 109 ASN Q 139 ASN S 86 GLN S 109 ASN U 109 ASN W 109 ASN W 125 ASN W 139 ASN X 109 ASN Y 109 ASN a 109 ASN a 125 ASN a 139 ASN e 109 ASN e 125 ASN r 109 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.164124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.156208 restraints weight = 19941.437| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.34 r_work: 0.3392 rms_B_bonded: 0.61 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work: 0.3024 rms_B_bonded: 3.51 restraints_weight: 0.1250 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1295 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= 0.187 Angle : 0.581 6.222 46848 Z= 0.311 Chirality : 0.038 0.139 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.394 19.123 4536 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.22 % Allowed : 7.03 % Favored : 92.76 % 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: 4.30 (0.13), residues: 4032 helix: 3.20 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 1.11 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP S 93 HIS 0.006 0.001 HIS I 128 PHE 0.013 0.002 PHE Y 41 TYR 0.019 0.003 TYR P 39 ARG 0.003 0.001 ARG A 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19805.29 seconds wall clock time: 352 minutes 4.56 seconds (21124.56 seconds total)