Starting phenix.real_space_refine on Sat Mar 23 06:13:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cps_16784/03_2024/8cps_16784_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cps_16784/03_2024/8cps_16784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cps_16784/03_2024/8cps_16784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cps_16784/03_2024/8cps_16784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cps_16784/03_2024/8cps_16784_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cps_16784/03_2024/8cps_16784_updated.pdb" } resolution = 1.82 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 8540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 116": "OE1" <-> "OE2" Residue "1 GLU 147": "OE1" <-> "OE2" Residue "2 GLU 107": "OE1" <-> "OE2" Residue "2 GLU 140": "OE1" <-> "OE2" Residue "2 GLU 147": "OE1" <-> "OE2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 116": "OE1" <-> "OE2" Residue "4 GLU 147": "OE1" <-> "OE2" Residue "6 GLU 94": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I ASP 123": "OD1" <-> "OD2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 107": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "Q GLU 147": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "W GLU 107": "OE1" <-> "OE2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "X GLU 107": "OE1" <-> "OE2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "Y GLU 107": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 140": "OE1" <-> "OE2" Residue "a GLU 147": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 147": "OE1" <-> "OE2" Residue "r GLU 107": "OE1" <-> "OE2" Residue "r GLU 116": "OE1" <-> "OE2" Residue "r ASP 123": "OD1" <-> "OD2" Residue "r GLU 140": "OE1" <-> "OE2" Residue "r GLU 147": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36034 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "2" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "4" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "6" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "M" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "O" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "P" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "Q" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "S" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} 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: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Y" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} 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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "r" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Time building chain proxies: 16.69, per 1000 atoms: 0.46 Number of scatterers: 36034 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 8540 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: 17.16 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 72.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain '1' and resid 14 through 41 Processing helix chain '1' and resid 49 through 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 2418 hydrogen bonds defined for protein. 7254 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: 11.24 Time building geometry restraints manager: 18.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11664 1.34 - 1.46: 5786 1.46 - 1.58: 17062 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX O 90 " pdb=" SG CSX O 90 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CSX e 90 " pdb=" SG CSX e 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CB CSX 6 90 " pdb=" SG CSX 6 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.28: 956 107.28 - 113.94: 19337 113.94 - 120.60: 13756 120.60 - 127.26: 12463 127.26 - 133.92: 336 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR E 39 " pdb=" CB TYR E 39 " pdb=" CG TYR E 39 " ideal model delta sigma weight residual 113.90 108.70 5.20 1.80e+00 3.09e-01 8.35e+00 angle pdb=" CA TYR I 39 " pdb=" CB TYR I 39 " pdb=" CG TYR I 39 " ideal model delta sigma weight residual 113.90 108.72 5.18 1.80e+00 3.09e-01 8.28e+00 angle pdb=" CA TYR 1 39 " pdb=" CB TYR 1 39 " pdb=" CG TYR 1 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" CA TYR Q 39 " pdb=" CB TYR Q 39 " pdb=" CG TYR Q 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" CA TYR M 39 " pdb=" CB TYR M 39 " pdb=" CG TYR M 39 " ideal model delta sigma weight residual 113.90 108.73 5.17 1.80e+00 3.09e-01 8.24e+00 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 19184 17.67 - 35.34: 1270 35.34 - 53.02: 323 53.02 - 70.69: 86 70.69 - 88.36: 137 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA VAL X 46 " pdb=" C VAL X 46 " pdb=" N ALA X 47 " pdb=" CA ALA X 47 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA VAL Q 46 " pdb=" C VAL Q 46 " pdb=" N ALA Q 47 " pdb=" CA ALA Q 47 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3644 0.043 - 0.085: 923 0.085 - 0.128: 252 0.128 - 0.171: 59 0.171 - 0.213: 42 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR K 137 " pdb=" N TYR K 137 " pdb=" C TYR K 137 " pdb=" CB TYR K 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA TYR O 137 " pdb=" N TYR O 137 " pdb=" C TYR O 137 " pdb=" CB TYR O 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA TYR P 137 " pdb=" N TYR P 137 " pdb=" C TYR P 137 " pdb=" CB TYR P 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 137 " -0.022 2.00e-02 2.50e+03 1.55e-02 4.81e+00 pdb=" CG TYR H 137 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR H 137 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 137 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR H 137 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR H 137 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Y 137 " 0.022 2.00e-02 2.50e+03 1.55e-02 4.80e+00 pdb=" CG TYR Y 137 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR Y 137 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR Y 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR Y 137 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR Y 137 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Y 137 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR Y 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 137 " -0.022 2.00e-02 2.50e+03 1.55e-02 4.78e+00 pdb=" CG TYR B 137 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 137 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 137 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 137 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 137 " -0.018 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1707 2.67 - 3.23: 37375 3.23 - 3.79: 70172 3.79 - 4.34: 94742 4.34 - 4.90: 146223 Nonbonded interactions: 350219 Sorted by model distance: nonbonded pdb=" OD1 ASP 1 123 " pdb=" O HOH 1 301 " model vdw 2.116 2.440 nonbonded pdb=" OD1 ASP e 123 " pdb=" O HOH e 601 " model vdw 2.116 2.440 nonbonded pdb=" OD1 ASP B 123 " pdb=" O HOH B 601 " model vdw 2.117 2.440 nonbonded pdb=" OD1 ASP A 123 " pdb=" O HOH A 601 " model vdw 2.117 2.440 nonbonded pdb=" OD1 ASP O 123 " pdb=" O HOH O 601 " model vdw 2.117 2.440 ... (remaining 350214 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) selection = (chain '2' and resid 4 through 176) selection = (chain '4' and resid 4 through 176) selection = (chain '6' and resid 4 through 176) selection = (chain 'A' and resid 4 through 176) selection = (chain 'B' and resid 4 through 176) selection = (chain 'E' and resid 4 through 176) selection = (chain 'F' and resid 4 through 176) selection = (chain 'G' and resid 4 through 176) selection = (chain 'H' and resid 4 through 176) selection = (chain 'I' and resid 4 through 176) selection = (chain 'K' and resid 4 through 176) selection = (chain 'M' and resid 4 through 176) selection = (chain 'O' and resid 4 through 176) selection = (chain 'P' and resid 4 through 176) selection = (chain 'Q' and resid 4 through 176) selection = (chain 'S' and resid 4 through 176) selection = (chain 'U' and resid 4 through 176) selection = (chain 'W' and resid 4 through 176) selection = (chain 'X' and resid 4 through 176) selection = (chain 'Y' and resid 4 through 176) selection = (chain 'a' and resid 4 through 176) selection = (chain 'e' and resid 4 through 176) selection = (chain 'r' and resid 4 through 176) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.030 Extract box with map and model: 7.790 Check model and map are aligned: 0.480 Set scattering table: 0.320 Process input model: 91.640 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.300 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.003 0.073 34776 Z= 0.223 Angle : 0.660 6.742 46848 Z= 0.373 Chirality : 0.045 0.213 4920 Planarity : 0.006 0.055 6192 Dihedral : 15.421 88.361 13032 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.28 (0.13), residues: 4032 helix: 1.70 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.94 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 93 HIS 0.009 0.002 HIS F 128 PHE 0.021 0.003 PHE I 41 TYR 0.029 0.004 TYR B 137 ARG 0.015 0.003 ARG r 76 *********************** 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 738 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 738 time to evaluate : 3.912 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 738 average time/residue: 2.0374 time to fit residues: 1726.0924 Evaluate side-chains 684 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 4.022 ------------------------------------------------------------------------------- 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: 9.9990 chunk 309 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 105 HIS 1 139 ASN 2 60 HIS 2 105 HIS 2 139 ASN 4 60 HIS 4 105 HIS 4 139 ASN 6 60 HIS 6 105 HIS 6 139 ASN A 105 HIS B 105 HIS E 83 GLN E 105 HIS E 139 ASN F 105 HIS G 83 GLN G 105 HIS H 83 GLN H 105 HIS H 139 ASN I 83 GLN I 105 HIS I 139 ASN K 60 HIS K 105 HIS K 139 ASN M 105 HIS M 139 ASN O 105 HIS O 139 ASN P 105 HIS P 139 ASN Q 105 HIS S 105 HIS U 60 HIS U 105 HIS U 139 ASN W 105 HIS X 105 HIS X 139 ASN Y 105 HIS Y 139 ASN a 105 HIS e 105 HIS e 139 ASN r 83 GLN r 105 HIS r 139 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.0764 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= 0.244 Angle : 0.670 6.427 46848 Z= 0.363 Chirality : 0.044 0.153 4920 Planarity : 0.004 0.021 6192 Dihedral : 5.196 34.912 4536 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 5.61 % 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: 4.11 (0.13), residues: 4032 helix: 3.04 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.18 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 93 HIS 0.006 0.001 HIS X 128 PHE 0.026 0.004 PHE A 41 TYR 0.028 0.004 TYR e 39 ARG 0.007 0.001 ARG 2 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 700 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 699 time to evaluate : 4.251 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 699 average time/residue: 2.0248 time to fit residues: 1623.5392 Evaluate side-chains 691 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 690 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 61 GLU 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: 0.2980 chunk 308 optimal weight: 0.1980 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 2.9990 chunk 400 optimal weight: 0.5980 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 297 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 4 60 HIS 4 83 GLN 6 60 HIS 6 83 GLN A 83 GLN B 83 GLN E 83 GLN F 83 GLN G 60 HIS G 83 GLN G 112 GLN H 83 GLN I 83 GLN K 60 HIS K 83 GLN M 112 GLN O 83 GLN P 83 GLN Q 83 GLN S 83 GLN U 60 HIS U 83 GLN X 83 GLN a 83 GLN e 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 34776 Z= 0.118 Angle : 0.482 5.468 46848 Z= 0.258 Chirality : 0.035 0.127 4920 Planarity : 0.002 0.019 6192 Dihedral : 4.425 20.679 4536 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 6.15 % 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: 5.28 (0.13), residues: 4032 helix: 3.91 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.27 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP W 93 HIS 0.003 0.000 HIS Y 128 PHE 0.013 0.002 PHE A 41 TYR 0.016 0.002 TYR r 39 ARG 0.003 0.000 ARG M 63 *********************** 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 705 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 704 time to evaluate : 4.145 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 704 average time/residue: 2.0106 time to fit residues: 1624.7217 Evaluate side-chains 660 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 4.116 ------------------------------------------------------------------------------- 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: 0.9980 chunk 279 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 1 141 GLN 2 60 HIS 2 86 GLN 2 105 HIS 2 141 GLN 4 83 GLN 4 86 GLN 4 105 HIS 6 83 GLN 6 86 GLN 6 105 HIS 6 141 GLN A 86 GLN A 105 HIS A 141 GLN B 86 GLN B 105 HIS B 141 GLN E 83 GLN E 86 GLN E 105 HIS E 141 GLN F 83 GLN F 86 GLN F 105 HIS F 141 GLN G 60 HIS G 86 GLN G 105 HIS G 141 GLN H 83 GLN H 86 GLN H 105 HIS H 141 GLN I 60 HIS I 83 GLN I 86 GLN I 105 HIS I 141 GLN K 86 GLN K 105 HIS K 141 GLN M 86 GLN M 105 HIS M 141 GLN O 83 GLN O 86 GLN O 105 HIS O 141 GLN P 83 GLN P 86 GLN P 105 HIS P 141 GLN Q 60 HIS Q 86 GLN Q 105 HIS Q 141 GLN S 83 GLN S 86 GLN S 105 HIS ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN U 86 GLN U 105 HIS U 141 GLN W 83 GLN W 86 GLN W 105 HIS W 141 GLN X 83 GLN X 86 GLN X 105 HIS Y 86 GLN Y 105 HIS Y 141 GLN a 86 GLN a 105 HIS a 141 GLN e 83 GLN e 86 GLN e 105 HIS e 141 GLN r 83 GLN r 86 GLN r 105 HIS r 141 GLN Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34776 Z= 0.208 Angle : 0.608 6.200 46848 Z= 0.330 Chirality : 0.041 0.134 4920 Planarity : 0.003 0.022 6192 Dihedral : 4.888 29.907 4536 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 7.16 % 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: 4.70 (0.13), residues: 4032 helix: 3.47 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.33 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 93 HIS 0.005 0.001 HIS Y 128 PHE 0.022 0.003 PHE E 41 TYR 0.026 0.003 TYR E 39 ARG 0.006 0.001 ARG K 63 *********************** 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 700 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 4.282 Fit side-chains REVERT: 2 156 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7553 (mtt180) REVERT: F 156 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7553 (mtt180) REVERT: G 156 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7558 (mtt180) REVERT: H 156 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7555 (mtt180) REVERT: I 156 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7556 (mtt180) REVERT: M 156 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7560 (mtt180) REVERT: P 156 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7549 (mtt180) REVERT: X 156 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7551 (mtt180) REVERT: Y 156 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7555 (mtt180) REVERT: a 156 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7556 (mtt180) REVERT: r 156 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7554 (mtt180) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 2.0062 time to fit residues: 1611.3258 Evaluate side-chains 694 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 694 time to evaluate : 4.075 ------------------------------------------------------------------------------- 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: 1.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 353 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 86 GLN 2 105 HIS 4 86 GLN 4 105 HIS 6 86 GLN 6 105 HIS A 86 GLN A 105 HIS B 86 GLN B 105 HIS E 83 GLN E 86 GLN E 105 HIS F 86 GLN F 105 HIS G 60 HIS G 86 GLN G 105 HIS H 83 GLN H 86 GLN H 105 HIS I 83 GLN I 86 GLN I 105 HIS K 86 GLN K 105 HIS M 86 GLN M 105 HIS M 141 GLN O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 86 GLN Q 105 HIS S 86 GLN S 105 HIS S 141 GLN U 86 GLN U 105 HIS W 86 GLN W 105 HIS W 141 GLN X 83 GLN X 86 GLN X 105 HIS Y 86 GLN Y 105 HIS a 86 GLN a 105 HIS a 141 GLN e 86 GLN e 105 HIS r 86 GLN r 105 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0967 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= 0.154 Angle : 0.526 5.373 46848 Z= 0.286 Chirality : 0.037 0.128 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.637 23.066 4536 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.00 (0.13), residues: 4032 helix: 3.71 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.25 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 93 HIS 0.003 0.001 HIS X 128 PHE 0.017 0.003 PHE A 41 TYR 0.021 0.002 TYR E 39 ARG 0.004 0.001 ARG K 63 *********************** 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 704 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 4.162 Fit side-chains REVERT: G 156 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7507 (mtt180) REVERT: a 156 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7505 (mtt180) outliers start: 0 outliers final: 0 residues processed: 704 average time/residue: 2.0422 time to fit residues: 1648.0278 Evaluate side-chains 694 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 694 time to evaluate : 4.084 ------------------------------------------------------------------------------- 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: 0.8980 chunk 355 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 2 86 GLN 4 83 GLN 4 86 GLN 4 105 HIS 4 141 GLN 6 83 GLN 6 86 GLN 6 141 GLN A 86 GLN B 86 GLN E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN G 60 HIS G 83 GLN G 86 GLN G 141 GLN H 83 GLN H 86 GLN I 83 GLN I 86 GLN K 83 GLN K 86 GLN M 86 GLN M 141 GLN O 83 GLN O 86 GLN P 83 GLN P 86 GLN Q 83 GLN Q 86 GLN Q 141 GLN S 83 GLN S 86 GLN S 141 GLN U 83 GLN U 86 GLN W 83 GLN W 86 GLN W 105 HIS W 141 GLN X 83 GLN X 86 GLN Y 86 GLN a 83 GLN a 86 GLN a 141 GLN e 83 GLN e 86 GLN r 83 GLN r 86 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1099 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= 0.120 Angle : 0.470 5.226 46848 Z= 0.254 Chirality : 0.035 0.124 4920 Planarity : 0.003 0.019 6192 Dihedral : 4.309 22.265 4536 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.11 % Allowed : 7.65 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.36 (0.13), residues: 4032 helix: 4.00 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.13 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 93 HIS 0.002 0.000 HIS K 128 PHE 0.012 0.002 PHE A 41 TYR 0.016 0.002 TYR r 39 ARG 0.004 0.000 ARG E 63 *********************** 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 765 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 761 time to evaluate : 4.220 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 761 average time/residue: 2.0246 time to fit residues: 1767.6832 Evaluate side-chains 703 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 702 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 7 GLN 1 83 GLN 1 86 GLN 1 105 HIS 1 139 ASN 1 141 GLN 2 86 GLN 2 105 HIS 2 139 ASN 2 141 GLN 4 86 GLN 4 105 HIS 4 139 ASN 6 86 GLN 6 105 HIS 6 141 GLN A 86 GLN A 105 HIS A 139 ASN A 141 GLN B 86 GLN B 105 HIS B 139 ASN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN E 105 HIS E 139 ASN E 141 GLN F 7 GLN F 86 GLN F 105 HIS F 139 ASN F 141 GLN G 60 HIS G 86 GLN G 105 HIS G 141 GLN H 83 GLN H 86 GLN H 105 HIS H 139 ASN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 GLN I 60 HIS I 83 GLN I 86 GLN I 105 HIS I 139 ASN I 141 GLN K 86 GLN K 105 HIS K 139 ASN K 141 GLN M 86 GLN M 105 HIS M 141 GLN O 7 GLN O 83 GLN O 86 GLN O 105 HIS O 139 ASN O 141 GLN P 86 GLN P 105 HIS P 139 ASN P 141 GLN Q 7 GLN Q 60 HIS Q 86 GLN Q 105 HIS Q 141 GLN S 86 GLN S 105 HIS S 139 ASN S 141 GLN U 83 GLN U 86 GLN U 105 HIS U 139 ASN U 141 GLN W 86 GLN W 105 HIS W 141 GLN X 7 GLN X 86 GLN X 105 HIS X 139 ASN Y 86 GLN Y 105 HIS Y 139 ASN Y 141 GLN a 86 GLN a 105 HIS a 141 GLN e 86 GLN e 105 HIS e 139 ASN e 141 GLN r 86 GLN r 105 HIS r 139 ASN r 141 GLN Total number of N/Q/H flips: 100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 34776 Z= 0.281 Angle : 0.699 7.111 46848 Z= 0.377 Chirality : 0.044 0.163 4920 Planarity : 0.004 0.033 6192 Dihedral : 5.009 31.576 4536 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.52 % Allowed : 7.63 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.13), residues: 4032 helix: 3.27 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.33 (0.29), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 93 HIS 0.005 0.001 HIS S 128 PHE 0.024 0.004 PHE O 41 TYR 0.029 0.004 TYR B 39 ARG 0.008 0.001 ARG U 63 *********************** 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 689 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 670 time to evaluate : 4.182 Fit side-chains outliers start: 19 outliers final: 0 residues processed: 670 average time/residue: 2.0446 time to fit residues: 1570.5472 Evaluate side-chains 677 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 677 time to evaluate : 4.334 ------------------------------------------------------------------------------- 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: 20.0000 chunk 234 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 86 GLN 2 105 HIS 4 83 GLN 4 86 GLN 4 105 HIS 6 83 GLN 6 86 GLN 6 105 HIS A 83 GLN A 86 GLN A 105 HIS B 83 GLN B 86 GLN B 105 HIS B 141 GLN E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN F 105 HIS G 60 HIS G 83 GLN G 86 GLN G 105 HIS H 86 GLN H 105 HIS H 141 GLN I 60 HIS I 83 GLN I 86 GLN I 105 HIS K 83 GLN K 86 GLN K 105 HIS M 83 GLN M 86 GLN M 105 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 60 HIS Q 83 GLN Q 86 GLN Q 105 HIS S 83 GLN S 86 GLN S 105 HIS U 83 GLN U 86 GLN U 105 HIS W 83 GLN W 86 GLN W 105 HIS X 83 GLN X 86 GLN X 105 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1069 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= 0.191 Angle : 0.596 8.353 46848 Z= 0.319 Chirality : 0.039 0.136 4920 Planarity : 0.003 0.024 6192 Dihedral : 4.733 24.604 4536 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.19 % Allowed : 7.71 % Favored : 92.10 % 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: 4.65 (0.13), residues: 4032 helix: 3.43 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.28 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 93 HIS 0.004 0.001 HIS X 128 PHE 0.020 0.003 PHE H 41 TYR 0.024 0.003 TYR H 39 ARG 0.006 0.001 ARG K 63 *********************** 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 701 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 694 time to evaluate : 4.047 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 694 average time/residue: 2.0488 time to fit residues: 1629.0524 Evaluate side-chains 684 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 4.339 ------------------------------------------------------------------------------- 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: 10.0000 chunk 376 optimal weight: 0.9980 chunk 343 optimal weight: 20.0000 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 chunk 365 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 83 GLN 2 86 GLN 2 105 HIS 4 83 GLN 4 86 GLN 4 105 HIS 4 141 GLN 6 83 GLN 6 86 GLN 6 105 HIS A 83 GLN A 86 GLN A 105 HIS B 83 GLN B 86 GLN B 105 HIS B 141 GLN E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN F 105 HIS G 83 GLN G 86 GLN G 105 HIS H 83 GLN H 86 GLN H 105 HIS H 141 GLN I 60 HIS I 83 GLN I 86 GLN I 105 HIS K 83 GLN K 86 GLN K 105 HIS M 83 GLN M 86 GLN M 105 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 60 HIS Q 83 GLN Q 86 GLN Q 105 HIS S 83 GLN S 86 GLN S 105 HIS U 83 GLN U 86 GLN U 105 HIS W 83 GLN W 86 GLN W 105 HIS X 83 GLN X 86 GLN X 105 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34776 Z= 0.185 Angle : 0.601 9.307 46848 Z= 0.321 Chirality : 0.039 0.161 4920 Planarity : 0.003 0.024 6192 Dihedral : 4.684 23.665 4536 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % 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: 4.69 (0.13), residues: 4032 helix: 3.46 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.27 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 93 HIS 0.004 0.001 HIS 1 128 PHE 0.019 0.003 PHE U 41 TYR 0.024 0.003 TYR Q 39 ARG 0.005 0.001 ARG E 63 *********************** 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 677 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 677 time to evaluate : 4.888 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 677 average time/residue: 2.0363 time to fit residues: 1584.9572 Evaluate side-chains 695 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 695 time to evaluate : 4.118 ------------------------------------------------------------------------------- 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: 0.9980 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.5980 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 83 GLN 2 86 GLN 2 105 HIS 4 83 GLN 4 86 GLN 4 105 HIS 4 141 GLN 6 83 GLN 6 86 GLN 6 105 HIS A 83 GLN A 86 GLN A 105 HIS B 83 GLN B 86 GLN B 105 HIS B 141 GLN E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN F 105 HIS G 83 GLN G 86 GLN G 105 HIS H 83 GLN H 86 GLN H 105 HIS H 141 GLN I 83 GLN I 86 GLN I 105 HIS K 83 GLN K 86 GLN K 105 HIS M 83 GLN M 86 GLN M 105 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 83 GLN Q 86 GLN Q 105 HIS S 83 GLN S 86 GLN S 105 HIS U 83 GLN U 86 GLN U 105 HIS W 83 GLN W 86 GLN W 105 HIS X 83 GLN X 86 GLN X 105 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1094 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= 0.199 Angle : 0.623 9.498 46848 Z= 0.334 Chirality : 0.040 0.167 4920 Planarity : 0.003 0.037 6192 Dihedral : 4.707 24.181 4536 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.13), residues: 4032 helix: 3.36 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.27 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 93 HIS 0.004 0.001 HIS Y 128 PHE 0.020 0.003 PHE e 41 TYR 0.025 0.003 TYR E 39 ARG 0.008 0.001 ARG K 63 ********************** 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 691 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 691 time to evaluate : 4.360 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 691 average time/residue: 2.0718 time to fit residues: 1639.9391 Evaluate side-chains 682 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 682 time to evaluate : 4.079 ------------------------------------------------------------------------------- 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: 3.9990 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 GLN 1 86 GLN 1 105 HIS 2 60 HIS 2 83 GLN 2 86 GLN 2 105 HIS 4 83 GLN 4 86 GLN 4 105 HIS 6 83 GLN 6 86 GLN 6 105 HIS A 83 GLN A 86 GLN A 105 HIS B 83 GLN B 86 GLN B 105 HIS E 83 GLN E 86 GLN E 105 HIS F 83 GLN F 86 GLN F 105 HIS G 60 HIS G 83 GLN G 86 GLN G 105 HIS H 83 GLN H 86 GLN H 105 HIS I 83 GLN I 86 GLN I 105 HIS K 83 GLN K 86 GLN K 105 HIS M 83 GLN M 86 GLN M 105 HIS O 83 GLN O 86 GLN O 105 HIS P 83 GLN P 86 GLN P 105 HIS Q 83 GLN Q 86 GLN Q 105 HIS S 83 GLN S 86 GLN S 105 HIS U 83 GLN U 86 GLN U 105 HIS W 83 GLN W 86 GLN W 105 HIS X 83 GLN X 86 GLN X 105 HIS Y 83 GLN Y 86 GLN Y 105 HIS a 83 GLN a 86 GLN a 105 HIS e 83 GLN e 86 GLN e 105 HIS r 83 GLN r 86 GLN r 105 HIS Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.156388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.149512 restraints weight = 19998.859| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 0.33 r_work: 0.3281 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2931 rms_B_bonded: 3.05 restraints_weight: 0.1250 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1079 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 : 0.603 9.493 46848 Z= 0.322 Chirality : 0.039 0.176 4920 Planarity : 0.003 0.034 6192 Dihedral : 4.641 22.370 4536 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.63 (0.13), residues: 4032 helix: 3.43 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.26 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 93 HIS 0.005 0.001 HIS 2 60 PHE 0.019 0.003 PHE 1 41 TYR 0.023 0.003 TYR E 39 ARG 0.010 0.001 ARG E 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21281.26 seconds wall clock time: 373 minutes 31.34 seconds (22411.34 seconds total)