Starting phenix.real_space_refine on Sat Mar 23 05:10:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpu_16786/03_2024/8cpu_16786_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpu_16786/03_2024/8cpu_16786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpu_16786/03_2024/8cpu_16786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpu_16786/03_2024/8cpu_16786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpu_16786/03_2024/8cpu_16786_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpu_16786/03_2024/8cpu_16786_updated.pdb" } resolution = 1.76 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 8329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ASP 91": "OD1" <-> "OD2" Residue "2 ASP 91": "OD1" <-> "OD2" Residue "2 ASP 92": "OD1" <-> "OD2" Residue "4 ASP 91": "OD1" <-> "OD2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 ASP 92": "OD1" <-> "OD2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "K ASP 91": "OD1" <-> "OD2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "O ASP 92": "OD1" <-> "OD2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "U ASP 91": "OD1" <-> "OD2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W ASP 91": "OD1" <-> "OD2" Residue "W ASP 92": "OD1" <-> "OD2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "a ASP 91": "OD1" <-> "OD2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "e ASP 91": "OD1" <-> "OD2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "r ASP 91": "OD1" <-> "OD2" Residue "r GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35823 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: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "2" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "4" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "6" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "F" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "H" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "K" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "M" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "O" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "P" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "Q" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "S" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "U" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "X" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "Y" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "a" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "e" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "r" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 18.82, per 1000 atoms: 0.53 Number of scatterers: 35823 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 8329 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: 17.63 Conformation dependent library (CDL) restraints added in 5.3 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: 5.27 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: 11.02 Time building geometry restraints manager: 18.32 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: 11640 1.34 - 1.46: 5131 1.46 - 1.57: 17741 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB CSX S 90 " pdb=" SG CSX S 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB CSX U 90 " pdb=" SG CSX U 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB CSX 1 90 " pdb=" SG CSX 1 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB CSX 2 90 " pdb=" SG CSX 2 90 " ideal model delta sigma weight residual 1.831 1.760 0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.23: 601 106.23 - 113.16: 18926 113.16 - 120.08: 12297 120.08 - 127.01: 14640 127.01 - 133.94: 384 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR Q 39 " pdb=" CB TYR Q 39 " pdb=" CG TYR Q 39 " ideal model delta sigma weight residual 113.90 108.33 5.57 1.80e+00 3.09e-01 9.57e+00 angle pdb=" CA TYR 4 39 " pdb=" CB TYR 4 39 " pdb=" CG TYR 4 39 " ideal model delta sigma weight residual 113.90 108.37 5.53 1.80e+00 3.09e-01 9.45e+00 angle pdb=" CA TYR W 39 " pdb=" CB TYR W 39 " pdb=" CG TYR W 39 " ideal model delta sigma weight residual 113.90 108.38 5.52 1.80e+00 3.09e-01 9.41e+00 angle pdb=" CA TYR r 39 " pdb=" CB TYR r 39 " pdb=" CG TYR r 39 " ideal model delta sigma weight residual 113.90 108.40 5.50 1.80e+00 3.09e-01 9.34e+00 angle pdb=" CA TYR F 39 " pdb=" CB TYR F 39 " pdb=" CG TYR F 39 " ideal model delta sigma weight residual 113.90 108.40 5.50 1.80e+00 3.09e-01 9.34e+00 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 19241 17.84 - 35.67: 1256 35.67 - 53.51: 336 53.51 - 71.34: 69 71.34 - 89.18: 98 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA ASP S 44 " pdb=" CB ASP S 44 " pdb=" CG ASP S 44 " pdb=" OD1 ASP S 44 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP K 44 " pdb=" CB ASP K 44 " pdb=" CG ASP K 44 " pdb=" OD1 ASP K 44 " ideal model delta sinusoidal sigma weight residual -30.00 -87.39 57.39 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP X 44 " pdb=" CB ASP X 44 " pdb=" CG ASP X 44 " pdb=" OD1 ASP X 44 " ideal model delta sinusoidal sigma weight residual -30.00 -87.39 57.39 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3623 0.046 - 0.092: 930 0.092 - 0.138: 276 0.138 - 0.185: 49 0.185 - 0.231: 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 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA TYR e 137 " pdb=" N TYR e 137 " pdb=" C TYR e 137 " pdb=" CB TYR e 137 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+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 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 32 " 0.041 2.00e-02 2.50e+03 3.48e-02 2.43e+01 pdb=" CG TYR H 32 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR H 32 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR H 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR H 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 32 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR H 32 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR H 32 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 32 " 0.041 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR Q 32 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 32 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 32 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR Q 32 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR Q 32 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " -0.041 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR F 32 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " -0.003 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 1009 2.56 - 3.15: 31141 3.15 - 3.73: 67850 3.73 - 4.32: 94065 4.32 - 4.90: 148733 Nonbonded interactions: 342798 Sorted by model distance: nonbonded pdb=" OD1 ASP G 131 " pdb=" O HOH G 301 " model vdw 1.976 2.440 nonbonded pdb=" OD1 ASP 6 131 " pdb=" O HOH 6 301 " model vdw 1.993 2.440 nonbonded pdb=" O HOH G 301 " pdb=" O HOH W 601 " model vdw 2.021 2.440 nonbonded pdb=" OD1 ASP W 131 " pdb=" O HOH W 601 " model vdw 2.041 2.440 nonbonded pdb=" O HOH 6 301 " pdb=" O HOH W 601 " model vdw 2.050 2.440 ... (remaining 342793 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: 4.070 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: 0.060 Extract box with map and model: 8.430 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 93.230 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.340 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 : 0.004 0.072 34776 Z= 0.273 Angle : 0.707 5.569 46848 Z= 0.403 Chirality : 0.050 0.231 4920 Planarity : 0.007 0.057 6192 Dihedral : 14.912 89.177 13032 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.13), residues: 4032 helix: 1.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.88 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 93 HIS 0.008 0.002 HIS P 128 PHE 0.023 0.003 PHE A 41 TYR 0.085 0.007 TYR H 32 ARG 0.016 0.003 ARG F 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 610 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 610 time to evaluate : 4.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 1.9559 time to fit residues: 1375.0595 Evaluate side-chains 571 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 4.077 ------------------------------------------------------------------------------- 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: 7.9990 chunk 309 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 319 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 2 112 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.0826 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= 0.227 Angle : 0.606 5.534 46848 Z= 0.336 Chirality : 0.040 0.151 4920 Planarity : 0.004 0.025 6192 Dihedral : 4.395 21.410 4536 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.06 % Allowed : 2.07 % Favored : 96.87 % 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: 3.91 (0.13), residues: 4032 helix: 2.98 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.76 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 93 HIS 0.005 0.002 HIS F 65 PHE 0.018 0.003 PHE Y 41 TYR 0.049 0.004 TYR 4 32 ARG 0.006 0.001 ARG W 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 630 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 591 time to evaluate : 4.632 Fit side-chains outliers start: 39 outliers final: 0 residues processed: 591 average time/residue: 2.1302 time to fit residues: 1435.2203 Evaluate side-chains 568 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 3.867 ------------------------------------------------------------------------------- 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: 8.9990 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 0.7980 chunk 400 optimal weight: 1.9990 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0958 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= 0.194 Angle : 0.560 5.738 46848 Z= 0.310 Chirality : 0.038 0.141 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.252 21.723 4536 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.53 % Favored : 96.81 % 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: 4.22 (0.13), residues: 4032 helix: 3.19 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.91 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 93 HIS 0.004 0.001 HIS 6 65 PHE 0.015 0.002 PHE Q 81 TYR 0.029 0.003 TYR A 32 ARG 0.005 0.001 ARG S 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 594 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 570 time to evaluate : 4.209 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 570 average time/residue: 2.1800 time to fit residues: 1411.6460 Evaluate side-chains 574 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 3.507 ------------------------------------------------------------------------------- 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: 5.9990 chunk 279 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 8.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1027 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= 0.226 Angle : 0.603 5.690 46848 Z= 0.331 Chirality : 0.038 0.136 4920 Planarity : 0.004 0.029 6192 Dihedral : 4.295 22.158 4536 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.65 % Allowed : 2.67 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.00 (0.12), residues: 4032 helix: 3.04 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.83 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 93 HIS 0.005 0.001 HIS A 65 PHE 0.017 0.003 PHE 4 81 TYR 0.024 0.003 TYR r 39 ARG 0.006 0.001 ARG 6 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 604 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 580 time to evaluate : 4.066 Fit side-chains outliers start: 24 outliers final: 1 residues processed: 580 average time/residue: 2.2239 time to fit residues: 1464.0082 Evaluate side-chains 576 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 575 time to evaluate : 3.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 14 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 5.9990 chunk 272 optimal weight: 0.0070 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34776 Z= 0.184 Angle : 0.544 5.161 46848 Z= 0.300 Chirality : 0.037 0.135 4920 Planarity : 0.003 0.033 6192 Dihedral : 4.228 22.020 4536 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.65 % Allowed : 2.40 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.26 (0.13), residues: 4032 helix: 3.23 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.89 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 93 HIS 0.003 0.001 HIS O 65 PHE 0.014 0.002 PHE P 81 TYR 0.021 0.003 TYR S 39 ARG 0.006 0.001 ARG I 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 590 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 566 time to evaluate : 3.906 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 566 average time/residue: 2.1821 time to fit residues: 1404.8819 Evaluate side-chains 570 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 4.091 ------------------------------------------------------------------------------- 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: 9.9990 chunk 355 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 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 86 GLN 1 112 GLN 2 86 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 34776 Z= 0.307 Angle : 0.702 5.973 46848 Z= 0.385 Chirality : 0.041 0.144 4920 Planarity : 0.005 0.042 6192 Dihedral : 4.397 22.222 4536 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 2.34 % Favored : 97.00 % 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: 3.44 (0.12), residues: 4032 helix: 2.68 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.47 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP M 93 HIS 0.006 0.002 HIS W 65 PHE 0.022 0.003 PHE X 81 TYR 0.029 0.004 TYR Q 39 ARG 0.010 0.001 ARG I 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 597 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 573 time to evaluate : 4.502 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 573 average time/residue: 2.1672 time to fit residues: 1414.8149 Evaluate side-chains 579 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 555 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain r residue 14 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 0.9980 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 2 86 GLN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN B 86 GLN B 112 GLN E 86 GLN F 86 GLN F 109 ASN F 112 GLN G 86 GLN H 86 GLN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN Q 86 GLN Q 109 ASN S 60 HIS S 86 GLN S 109 ASN U 86 GLN W 86 GLN X 86 GLN Y 86 GLN Y 112 GLN a 86 GLN e 86 GLN e 112 GLN r 86 GLN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34776 Z= 0.146 Angle : 0.493 4.969 46848 Z= 0.274 Chirality : 0.035 0.134 4920 Planarity : 0.003 0.017 6192 Dihedral : 4.178 21.819 4536 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 2.51 % Favored : 96.84 % 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: 4.44 (0.13), residues: 4032 helix: 3.38 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.81 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 93 HIS 0.002 0.001 HIS H 118 PHE 0.011 0.002 PHE 6 132 TYR 0.019 0.002 TYR S 39 ARG 0.003 0.000 ARG X 156 *********************** 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 644 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 620 time to evaluate : 3.860 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 620 average time/residue: 2.0585 time to fit residues: 1461.6508 Evaluate side-chains 567 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 567 time to evaluate : 4.133 ------------------------------------------------------------------------------- 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: 1.9990 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 1 139 ASN 2 86 GLN 2 139 ASN 4 86 GLN 4 112 GLN 4 139 ASN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN A 139 ASN B 86 GLN B 112 GLN B 139 ASN E 86 GLN E 139 ASN F 86 GLN F 109 ASN F 112 GLN G 60 HIS G 86 GLN H 86 GLN H 139 ASN I 60 HIS I 86 GLN I 112 GLN I 139 ASN K 86 GLN K 112 GLN K 139 ASN M 86 GLN M 139 ASN O 86 GLN O 139 ASN P 86 GLN P 139 ASN Q 86 GLN Q 109 ASN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 GLN S 109 ASN U 60 HIS U 86 GLN U 139 ASN W 86 GLN W 139 ASN X 86 GLN X 139 ASN Y 86 GLN Y 112 GLN Y 139 ASN a 60 HIS a 86 GLN a 139 ASN e 60 HIS e 86 GLN e 112 GLN e 139 ASN r 86 GLN r 112 GLN r 139 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 34776 Z= 0.126 Angle : 0.458 4.625 46848 Z= 0.254 Chirality : 0.034 0.130 4920 Planarity : 0.003 0.017 6192 Dihedral : 4.071 21.794 4536 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 3.38 % Favored : 95.97 % 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: 4.88 (0.13), residues: 4032 helix: 3.69 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.93 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 93 HIS 0.002 0.001 HIS I 128 PHE 0.012 0.002 PHE 6 132 TYR 0.016 0.002 TYR E 39 ARG 0.002 0.000 ARG E 156 *********************** 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 612 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 588 time to evaluate : 4.198 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 588 average time/residue: 2.0996 time to fit residues: 1409.1893 Evaluate side-chains 549 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 4.187 ------------------------------------------------------------------------------- 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: 0.5980 chunk 376 optimal weight: 0.9980 chunk 343 optimal weight: 0.9990 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 287 optimal weight: 0.4980 chunk 112 optimal weight: 8.9990 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 365 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 112 GLN 1 139 ASN 2 86 GLN 2 139 ASN 4 86 GLN 4 112 GLN 6 86 GLN 6 109 ASN A 86 GLN A 112 GLN A 139 ASN B 86 GLN B 112 GLN B 139 ASN E 86 GLN E 139 ASN F 86 GLN F 109 ASN F 112 GLN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN H 86 GLN H 139 ASN I 86 GLN I 112 GLN K 86 GLN K 112 GLN M 86 GLN O 86 GLN P 86 GLN P 139 ASN Q 86 GLN Q 109 ASN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 GLN S 109 ASN S 139 ASN ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN W 86 GLN X 86 GLN X 139 ASN Y 86 GLN Y 112 GLN ** a 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN a 139 ASN ** e 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 GLN e 112 GLN r 86 GLN r 112 GLN r 139 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34776 Z= 0.111 Angle : 0.433 4.358 46848 Z= 0.241 Chirality : 0.034 0.137 4920 Planarity : 0.002 0.019 6192 Dihedral : 3.991 21.507 4536 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 3.54 % Favored : 95.81 % 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: 5.16 (0.13), residues: 4032 helix: 3.90 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.94 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 93 HIS 0.002 0.000 HIS 6 128 PHE 0.012 0.002 PHE G 132 TYR 0.016 0.002 TYR I 39 ARG 0.001 0.000 ARG G 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 602 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 578 time to evaluate : 4.138 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 578 average time/residue: 2.0888 time to fit residues: 1378.5216 Evaluate side-chains 551 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 4.193 ------------------------------------------------------------------------------- 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: 9.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 406 optimal weight: 2.9990 chunk 374 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 139 ASN 2 86 GLN 2 139 ASN 4 86 GLN 4 139 ASN 6 86 GLN 6 109 ASN 6 139 ASN A 60 HIS A 86 GLN A 139 ASN B 60 HIS B 86 GLN B 139 ASN E 86 GLN E 139 ASN F 86 GLN F 109 ASN F 139 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN G 139 ASN H 86 GLN H 139 ASN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN I 139 ASN K 86 GLN K 139 ASN M 86 GLN M 139 ASN O 86 GLN O 139 ASN P 86 GLN P 139 ASN Q 86 GLN Q 109 ASN Q 139 ASN S 60 HIS S 86 GLN S 109 ASN S 139 ASN ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN U 139 ASN W 86 GLN X 86 GLN X 139 ASN Y 86 GLN Y 139 ASN a 60 HIS a 86 GLN a 139 ASN e 60 HIS e 86 GLN e 139 ASN r 86 GLN r 139 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1145 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= 0.168 Angle : 0.520 4.802 46848 Z= 0.289 Chirality : 0.037 0.139 4920 Planarity : 0.003 0.020 6192 Dihedral : 4.187 22.874 4536 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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: 4.61 (0.13), residues: 4032 helix: 3.48 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.95 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 93 HIS 0.003 0.001 HIS S 65 PHE 0.014 0.002 PHE 6 81 TYR 0.027 0.002 TYR a 39 ARG 0.003 0.000 ARG K 156 ********************** 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 565 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 565 time to evaluate : 4.151 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 565 average time/residue: 2.2237 time to fit residues: 1439.8027 Evaluate side-chains 569 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 4.650 ------------------------------------------------------------------------------- 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: 10.0000 chunk 344 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 332 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 86 GLN 1 139 ASN 2 86 GLN 2 139 ASN 4 86 GLN 4 139 ASN 6 86 GLN 6 109 ASN 6 139 ASN ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN A 139 ASN B 60 HIS B 86 GLN B 139 ASN E 60 HIS E 86 GLN E 139 ASN F 86 GLN F 109 ASN F 139 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN H 86 GLN H 139 ASN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN I 139 ASN K 86 GLN K 139 ASN M 60 HIS M 86 GLN M 139 ASN O 86 GLN O 139 ASN P 86 GLN P 139 ASN Q 86 GLN Q 109 ASN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 GLN S 109 ASN S 139 ASN ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN U 139 ASN W 86 GLN X 86 GLN X 139 ASN Y 86 GLN Y 139 ASN ** a 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN a 139 ASN ** e 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 GLN e 139 ASN r 60 HIS r 86 GLN r 139 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.151176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.144515 restraints weight = 18291.676| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 0.27 r_work: 0.3350 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 1.01 restraints_weight: 0.2500 r_work: 0.2991 rms_B_bonded: 2.93 restraints_weight: 0.1250 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 34776 Z= 0.162 Angle : 0.521 4.709 46848 Z= 0.289 Chirality : 0.036 0.141 4920 Planarity : 0.003 0.021 6192 Dihedral : 4.183 22.795 4536 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: 4.57 (0.13), residues: 4032 helix: 3.46 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.92 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 93 HIS 0.002 0.001 HIS F 118 PHE 0.012 0.002 PHE O 81 TYR 0.026 0.002 TYR B 39 ARG 0.004 0.000 ARG S 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19303.54 seconds wall clock time: 339 minutes 16.56 seconds (20356.56 seconds total)