Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 07:25:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddq_30656/10_2023/7ddq_30656_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddq_30656/10_2023/7ddq_30656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddq_30656/10_2023/7ddq_30656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddq_30656/10_2023/7ddq_30656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddq_30656/10_2023/7ddq_30656_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddq_30656/10_2023/7ddq_30656_updated.pdb" } resolution = 2.84 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= 0.003 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 34 5.21 5 S 84 5.16 5 C 15792 2.51 5 N 3246 2.21 5 O 3411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 45": "OD1" <-> "OD2" Residue "N PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 13": "OD1" <-> "OD2" Residue "N TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 12": "OD1" <-> "OD2" Residue "S PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "b TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 45": "OD1" <-> "OD2" Residue "A ASP 13": "OD1" <-> "OD2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 45": "OD1" <-> "OD2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 12": "OD1" <-> "OD2" Residue "u PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X ASP 71": "OD1" <-> "OD2" Residue "X ARG 80": "NH1" <-> "NH2" Residue "s PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 45": "OD1" <-> "OD2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "i PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 45": "OD1" <-> "OD2" Residue "j TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 52": "OE1" <-> "OE2" Residue "I PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 156": "OE1" <-> "OE2" Residue "L TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 202": "OE1" <-> "OE2" Residue "L GLU 206": "OE1" <-> "OE2" Residue "L PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 3": "OE1" <-> "OE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M GLU 101": "OE1" <-> "OE2" Residue "M GLU 293": "OE1" <-> "OE2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "g PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 45": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 22571 Number of models: 1 Model: "" Number of chains: 64 Chain: "o" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "N" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "t" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "S" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "r" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "O" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "a" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "U" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "e" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "A" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "k" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "J" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "f" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "E" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "u" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 440 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "T" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "X" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "s" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "R" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "n" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "K" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "G" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "j" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "I" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "L" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2188 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain: "M" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2420 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "H" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1907 Classifications: {'peptide': 250} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 230} Chain: "g" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "B" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "o" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 114 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 275 Unusual residues: {'BCL': 1, 'BPH': 2, 'U10': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'BPH:plan-1': 1, 'U10:plan-8': 3, 'U10:plan-9': 3, 'U10:plan-5': 1, 'U10:plan-6': 2, 'U10:plan-7': 3, 'U10:plan-10': 3, 'U10:plan-11': 3} Unresolved non-hydrogen planarities: 77 Chain: "M" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 372 Unusual residues: {' FE': 1, 'BCL': 3, 'BPH': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'3PE': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.19, per 1000 atoms: 0.54 Number of scatterers: 22571 At special positions: 0 Unit cell: (118.69, 132.8, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 84 16.00 P 3 15.00 Mg 34 11.99 O 3411 8.00 N 3246 7.00 C 15792 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=34, symmetry=0 Number of additional bonds: simple=34, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.62 Conformation dependent library (CDL) restraints added in 2.7 seconds 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4364 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 4 sheets defined 64.9% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'o' and resid 4 through 10 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'N' and resid 13 through 44 Processing helix chain 't' and resid 4 through 9 Processing helix chain 't' and resid 13 through 37 Processing helix chain 't' and resid 43 through 50 Processing helix chain 'S' and resid 13 through 44 removed outlier: 3.865A pdb=" N GLN S 17 " --> pdb=" O ASP S 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU S 18 " --> pdb=" O GLN S 14 " (cutoff:3.500A) Processing helix chain 'r' and resid 4 through 10 Processing helix chain 'r' and resid 13 through 37 Processing helix chain 'r' and resid 43 through 50 Processing helix chain 'O' and resid 13 through 44 Processing helix chain 'a' and resid 4 through 9 Processing helix chain 'a' and resid 13 through 37 Processing helix chain 'a' and resid 39 through 41 No H-bonds generated for 'chain 'a' and resid 39 through 41' Processing helix chain 'U' and resid 13 through 43 Processing helix chain 'e' and resid 4 through 9 Processing helix chain 'e' and resid 13 through 37 Processing helix chain 'e' and resid 43 through 50 Processing helix chain 'D' and resid 13 through 44 Processing helix chain 'b' and resid 4 through 9 Processing helix chain 'b' and resid 13 through 37 Processing helix chain 'b' and resid 43 through 50 Processing helix chain 'A' and resid 13 through 44 Processing helix chain 'k' and resid 4 through 10 Processing helix chain 'k' and resid 13 through 37 Processing helix chain 'k' and resid 43 through 50 Processing helix chain 'J' and resid 13 through 44 removed outlier: 3.541A pdb=" N GLN J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 9 removed outlier: 3.501A pdb=" N ILE f 7 " --> pdb=" O PHE f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 37 Processing helix chain 'f' and resid 43 through 50 Processing helix chain 'E' and resid 13 through 44 Processing helix chain 'u' and resid 4 through 10 Processing helix chain 'u' and resid 13 through 37 Processing helix chain 'u' and resid 43 through 50 Processing helix chain 'T' and resid 13 through 44 removed outlier: 3.538A pdb=" N GLU T 18 " --> pdb=" O GLN T 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 50 removed outlier: 3.809A pdb=" N PHE X 50 " --> pdb=" O PHE X 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 56 Processing helix chain 's' and resid 4 through 9 Processing helix chain 's' and resid 13 through 37 Processing helix chain 's' and resid 43 through 50 Processing helix chain 'R' and resid 13 through 44 removed outlier: 3.732A pdb=" N GLN R 17 " --> pdb=" O ASP R 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU R 18 " --> pdb=" O GLN R 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 9 Processing helix chain 'n' and resid 13 through 37 Processing helix chain 'n' and resid 43 through 50 Processing helix chain 'K' and resid 13 through 44 Processing helix chain 'i' and resid 4 through 9 Processing helix chain 'i' and resid 13 through 37 Processing helix chain 'i' and resid 43 through 50 Processing helix chain 'G' and resid 13 through 44 Processing helix chain 'j' and resid 4 through 9 Processing helix chain 'j' and resid 13 through 37 Processing helix chain 'j' and resid 43 through 50 Processing helix chain 'I' and resid 13 through 44 removed outlier: 3.504A pdb=" N GLN I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 72 through 74 No H-bonds generated for 'chain 'L' and resid 72 through 74' Processing helix chain 'L' and resid 85 through 111 Processing helix chain 'L' and resid 117 through 133 Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 143 through 145 No H-bonds generated for 'chain 'L' and resid 143 through 145' Processing helix chain 'L' and resid 153 through 165 removed outlier: 3.873A pdb=" N TYR L 165 " --> pdb=" O VAL L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 170 No H-bonds generated for 'chain 'L' and resid 168 through 170' Processing helix chain 'L' and resid 172 through 199 Processing helix chain 'L' and resid 210 through 221 Processing helix chain 'L' and resid 227 through 251 removed outlier: 3.848A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 268 Processing helix chain 'M' and resid 27 through 29 No H-bonds generated for 'chain 'M' and resid 27 through 29' Processing helix chain 'M' and resid 38 through 41 No H-bonds generated for 'chain 'M' and resid 38 through 41' Processing helix chain 'M' and resid 55 through 78 Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 114 through 141 removed outlier: 3.503A pdb=" N ALA M 138 " --> pdb=" O THR M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 162 Processing helix chain 'M' and resid 164 through 169 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 180 through 193 removed outlier: 3.890A pdb=" N LEU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 199 No H-bonds generated for 'chain 'M' and resid 197 through 199' Processing helix chain 'M' and resid 201 through 226 Processing helix chain 'M' and resid 235 through 238 No H-bonds generated for 'chain 'M' and resid 235 through 238' Processing helix chain 'M' and resid 244 through 257 removed outlier: 3.547A pdb=" N TRP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 287 removed outlier: 4.429A pdb=" N HIS M 267 " --> pdb=" O MET M 263 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG M 268 " --> pdb=" O GLU M 264 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR M 277 " --> pdb=" O PHE M 273 " (cutoff:3.500A) Proline residue: M 278 - end of helix Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 134 through 137 No H-bonds generated for 'chain 'H' and resid 134 through 137' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 212 through 215 Processing helix chain 'H' and resid 227 through 243 removed outlier: 4.233A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 247 No H-bonds generated for 'chain 'H' and resid 245 through 247' Processing helix chain 'g' and resid 4 through 9 Processing helix chain 'g' and resid 13 through 37 Processing helix chain 'g' and resid 43 through 50 Processing helix chain 'F' and resid 13 through 44 Processing helix chain 'd' and resid 4 through 10 Processing helix chain 'd' and resid 13 through 37 Processing helix chain 'd' and resid 43 through 50 Processing helix chain 'B' and resid 13 through 44 Processing sheet with id= A, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.737A pdb=" N GLU H 180 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET H 167 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR H 178 " --> pdb=" O MET H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.762A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3297 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: 5.82 Time building geometry restraints manager: 11.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.32: 3417 1.32 - 1.53: 18460 1.53 - 1.74: 1290 1.74 - 1.96: 162 1.96 - 2.17: 136 Bond restraints: 23465 Sorted by residual: bond pdb=" C14 SPO E 201 " pdb=" C15 SPO E 201 " ideal model delta sigma weight residual 1.435 1.566 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C14 SPO M 406 " pdb=" C15 SPO M 406 " ideal model delta sigma weight residual 1.435 1.564 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C14 SPO g 102 " pdb=" C15 SPO g 102 " ideal model delta sigma weight residual 1.435 1.560 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C19 SPO E 201 " pdb=" C20 SPO E 201 " ideal model delta sigma weight residual 1.435 1.559 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C19 SPO g 102 " pdb=" C20 SPO g 102 " ideal model delta sigma weight residual 1.435 1.556 -0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 23460 not shown) Histogram of bond angle deviations from ideal: 74.66 - 92.40: 176 92.40 - 110.14: 4666 110.14 - 127.88: 26474 127.88 - 145.62: 904 145.62 - 163.36: 97 Bond angle restraints: 32317 Sorted by residual: angle pdb=" C4 SPO j 301 " pdb=" C1 SPO j 301 " pdb=" O1 SPO j 301 " ideal model delta sigma weight residual 104.58 144.99 -40.41 3.00e+00 1.11e-01 1.81e+02 angle pdb=" C4 SPO X 201 " pdb=" C1 SPO X 201 " pdb=" O1 SPO X 201 " ideal model delta sigma weight residual 104.58 143.97 -39.39 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C4 SPO F 102 " pdb=" C1 SPO F 102 " pdb=" O1 SPO F 102 " ideal model delta sigma weight residual 104.58 143.02 -38.44 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C4 SPO t 102 " pdb=" C1 SPO t 102 " pdb=" O1 SPO t 102 " ideal model delta sigma weight residual 104.58 139.93 -35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C3 SPO N 201 " pdb=" C1 SPO N 201 " pdb=" C4 SPO N 201 " ideal model delta sigma weight residual 108.79 74.66 34.13 3.00e+00 1.11e-01 1.29e+02 ... (remaining 32312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 11995 35.99 - 71.98: 315 71.98 - 107.96: 56 107.96 - 143.95: 7 143.95 - 179.94: 31 Dihedral angle restraints: 12404 sinusoidal: 5647 harmonic: 6757 Sorted by residual: dihedral pdb=" C1 BCL j 302 " pdb=" C2 BCL j 302 " pdb=" C3 BCL j 302 " pdb=" C5 BCL j 302 " ideal model delta sinusoidal sigma weight residual -180.00 -0.06 -179.94 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL r 101 " pdb=" C2 BCL r 101 " pdb=" C3 BCL r 101 " pdb=" C5 BCL r 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.07 -179.93 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL u 102 " pdb=" C2 BCL u 102 " pdb=" C3 BCL u 102 " pdb=" C5 BCL u 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.08 -179.92 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 12401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2826 0.075 - 0.150: 370 0.150 - 0.225: 30 0.225 - 0.300: 13 0.300 - 0.375: 3 Chirality restraints: 3242 Sorted by residual: chirality pdb=" CBD BCL b 101 " pdb=" CAD BCL b 101 " pdb=" CGD BCL b 101 " pdb=" CHA BCL b 101 " both_signs ideal model delta sigma weight residual False 2.62 2.25 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB VAL M 160 " pdb=" CA VAL M 160 " pdb=" CG1 VAL M 160 " pdb=" CG2 VAL M 160 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C2C BPH L 302 " pdb=" C1C BPH L 302 " pdb=" C3C BPH L 302 " pdb=" CMC BPH L 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.49 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 3239 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH L 306 " 0.014 2.00e-02 2.50e+03 6.17e-02 8.55e+01 pdb=" C1D BPH L 306 " 0.017 2.00e-02 2.50e+03 pdb=" C2D BPH L 306 " -0.031 2.00e-02 2.50e+03 pdb=" C3D BPH L 306 " -0.048 2.00e-02 2.50e+03 pdb=" C4D BPH L 306 " -0.030 2.00e-02 2.50e+03 pdb=" CAD BPH L 306 " 0.137 2.00e-02 2.50e+03 pdb=" CHA BPH L 306 " -0.060 2.00e-02 2.50e+03 pdb=" CHD BPH L 306 " 0.060 2.00e-02 2.50e+03 pdb=" CMD BPH L 306 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 273 " 0.052 2.00e-02 2.50e+03 5.60e-02 7.85e+01 pdb=" CG TRP L 273 " -0.144 2.00e-02 2.50e+03 pdb=" CD1 TRP L 273 " 0.086 2.00e-02 2.50e+03 pdb=" CD2 TRP L 273 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP L 273 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP L 273 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP L 273 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 273 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 273 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP L 273 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 217 " -0.067 2.00e-02 2.50e+03 5.88e-02 6.05e+01 pdb=" CG PHE M 217 " 0.132 2.00e-02 2.50e+03 pdb=" CD1 PHE M 217 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE M 217 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE M 217 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE M 217 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE M 217 " -0.014 2.00e-02 2.50e+03 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 51 2.34 - 2.98: 10860 2.98 - 3.62: 35004 3.62 - 4.26: 57367 4.26 - 4.90: 91950 Nonbonded interactions: 195232 Sorted by model distance: nonbonded pdb=" OE2 GLU M 235 " pdb="FE FE M 404 " model vdw 1.706 2.260 nonbonded pdb=" OG1 THR O 12 " pdb=" OE1 GLN O 15 " model vdw 2.019 2.440 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 404 " model vdw 2.083 2.340 nonbonded pdb=" OE1 GLN N 25 " pdb=" OG SER k 2 " model vdw 2.135 2.440 nonbonded pdb=" OD1 ASP T 13 " pdb=" NE2 GLN T 17 " model vdw 2.177 2.520 ... (remaining 195227 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 'A' and resid 5 through 47) selection = (chain 'B' and resid 5 through 47) selection = (chain 'D' and resid 5 through 47) selection = (chain 'E' and resid 5 through 47) selection = (chain 'F' and resid 5 through 47) selection = (chain 'G' and resid 5 through 47) selection = (chain 'I' and resid 5 through 47) selection = (chain 'J' and resid 5 through 47) selection = (chain 'K' and resid 5 through 47) selection = (chain 'N' and resid 5 through 47) selection = (chain 'O' and resid 5 through 47) selection = (chain 'R' and resid 5 through 47) selection = (chain 'S' and resid 5 through 47) selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'a' and resid 3 through 45) selection = (chain 'e' and resid 3 through 45) selection = (chain 'f' and resid 3 through 45) selection = (chain 'i' and resid 3 through 45) selection = (chain 'n' and resid 3 through 45) selection = (chain 'o' and resid 3 through 45) selection = (chain 'u' and resid 3 through 45) } ncs_group { reference = (chain 'b' and resid 2 through 54) selection = (chain 'd' and resid 2 through 54) selection = (chain 'g' and resid 2 through 54) selection = (chain 'j' and resid 2 through 54) selection = (chain 'k' and resid 2 through 54) selection = (chain 'r' and resid 2 through 54) selection = (chain 's' and resid 2 through 54) selection = (chain 't' and resid 2 through 54) } 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: 0.010 Normalize map: mean=0, sd=1: 0.840 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: 0.020 Extract box with map and model: 5.010 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 59.150 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.100 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.012 0.131 23465 Z= 0.671 Angle : 1.916 40.405 32317 Z= 0.692 Chirality : 0.055 0.375 3242 Planarity : 0.005 0.062 3934 Dihedral : 20.420 179.938 8040 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.05 (0.17), residues: 2286 helix: 1.64 (0.12), residues: 1519 sheet: 1.24 (1.04), residues: 22 loop : -1.33 (0.23), residues: 745 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 637 average time/residue: 1.1055 time to fit residues: 821.6724 Evaluate side-chains 480 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 477 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.2828 time to fit residues: 3.9209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 130 optimal weight: 0.0870 chunk 203 optimal weight: 5.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 20 GLN r 42 ASN O 25 GLN e 20 GLN b 20 GLN k 20 GLN k 42 ASN J 17 GLN f 20 GLN T 15 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN I 17 GLN L 68 ASN L 148 GLN L 200 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN F 17 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23465 Z= 0.226 Angle : 1.402 37.879 32317 Z= 0.509 Chirality : 0.040 0.369 3242 Planarity : 0.004 0.051 3934 Dihedral : 22.959 179.980 3821 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.25 % Allowed : 11.89 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.68 (0.17), residues: 2286 helix: 1.92 (0.12), residues: 1577 sheet: 1.78 (1.07), residues: 22 loop : -0.82 (0.24), residues: 687 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 544 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 18 residues processed: 560 average time/residue: 1.0918 time to fit residues: 718.7249 Evaluate side-chains 493 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 475 time to evaluate : 2.466 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 9 residues processed: 14 average time/residue: 0.4092 time to fit residues: 11.3845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 202 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN o 42 ASN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 ASN ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN f 20 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 23465 Z= 0.242 Angle : 1.314 40.883 32317 Z= 0.480 Chirality : 0.040 0.328 3242 Planarity : 0.004 0.053 3934 Dihedral : 22.565 179.953 3821 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.40 % Allowed : 13.84 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.89 (0.18), residues: 2286 helix: 2.16 (0.13), residues: 1564 sheet: 2.10 (1.03), residues: 26 loop : -0.92 (0.24), residues: 696 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 524 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 19 residues processed: 544 average time/residue: 1.1047 time to fit residues: 703.2029 Evaluate side-chains 489 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 470 time to evaluate : 2.401 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 9 residues processed: 12 average time/residue: 0.3511 time to fit residues: 9.6924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 193 optimal weight: 0.0770 chunk 58 optimal weight: 10.0000 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN N 15 GLN e 20 GLN f 38 ASN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23465 Z= 0.219 Angle : 1.249 37.319 32317 Z= 0.461 Chirality : 0.041 0.414 3242 Planarity : 0.003 0.051 3934 Dihedral : 22.391 179.936 3821 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.00 % Allowed : 16.14 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 2.04 (0.18), residues: 2286 helix: 2.27 (0.13), residues: 1550 sheet: 2.25 (1.01), residues: 26 loop : -0.79 (0.25), residues: 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 515 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 14 residues processed: 536 average time/residue: 1.0580 time to fit residues: 666.6711 Evaluate side-chains 482 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 468 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 5 average time/residue: 0.5501 time to fit residues: 6.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 184 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 110 optimal weight: 4.9990 chunk 194 optimal weight: 0.0040 chunk 54 optimal weight: 7.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN k 42 ASN f 20 GLN L 61 ASN L 160 ASN M 188 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 23465 Z= 0.247 Angle : 1.241 39.898 32317 Z= 0.462 Chirality : 0.041 0.340 3242 Planarity : 0.003 0.053 3934 Dihedral : 22.200 179.990 3821 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.20 % Allowed : 16.99 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.98 (0.18), residues: 2286 helix: 2.20 (0.13), residues: 1564 sheet: 3.02 (1.01), residues: 20 loop : -0.83 (0.24), residues: 702 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 508 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 28 residues processed: 533 average time/residue: 1.1141 time to fit residues: 695.8255 Evaluate side-chains 493 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 465 time to evaluate : 2.486 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 15 residues processed: 15 average time/residue: 0.5764 time to fit residues: 14.4214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.2980 chunk 194 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN r 42 ASN e 20 GLN b 42 ASN A 25 GLN ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 GLN f 20 GLN T 15 GLN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23465 Z= 0.247 Angle : 1.136 38.141 32317 Z= 0.434 Chirality : 0.041 0.360 3242 Planarity : 0.003 0.053 3934 Dihedral : 22.108 179.996 3821 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.90 % Allowed : 18.89 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.98 (0.18), residues: 2286 helix: 2.19 (0.13), residues: 1559 sheet: 2.26 (0.97), residues: 26 loop : -0.80 (0.25), residues: 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 488 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 26 residues processed: 514 average time/residue: 1.0820 time to fit residues: 653.1170 Evaluate side-chains 494 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 468 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 9 average time/residue: 0.3562 time to fit residues: 7.7735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 0.4980 chunk 135 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN a 20 GLN e 20 GLN b 38 ASN b 42 ASN A 25 GLN k 42 ASN f 20 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23465 Z= 0.218 Angle : 1.126 38.178 32317 Z= 0.433 Chirality : 0.041 0.383 3242 Planarity : 0.003 0.053 3934 Dihedral : 22.023 179.985 3821 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.90 % Allowed : 19.74 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.95 (0.18), residues: 2286 helix: 2.14 (0.13), residues: 1566 sheet: 2.95 (0.98), residues: 20 loop : -0.75 (0.25), residues: 700 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 502 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 26 residues processed: 529 average time/residue: 1.1130 time to fit residues: 693.1185 Evaluate side-chains 490 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 464 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 4 average time/residue: 0.2963 time to fit residues: 5.0680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN o 42 ASN r 42 ASN e 20 GLN ** e 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN f 20 GLN n 42 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN g 20 GLN d 20 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 23465 Z= 0.213 Angle : 1.140 38.226 32317 Z= 0.444 Chirality : 0.041 0.385 3242 Planarity : 0.003 0.052 3934 Dihedral : 21.912 179.972 3821 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.30 % Allowed : 21.04 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.78 (0.18), residues: 2286 helix: 1.98 (0.13), residues: 1579 sheet: 2.86 (0.99), residues: 20 loop : -0.79 (0.25), residues: 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 500 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 22 residues processed: 528 average time/residue: 1.0739 time to fit residues: 667.8200 Evaluate side-chains 485 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 463 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 1.0820 time to fit residues: 5.5180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 188 optimal weight: 0.0170 chunk 201 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 87 optimal weight: 0.0570 chunk 157 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 190 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 overall best weight: 2.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN o 42 ASN r 42 ASN e 20 GLN e 42 ASN ** f 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN g 20 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23465 Z= 0.259 Angle : 1.164 38.474 32317 Z= 0.458 Chirality : 0.044 0.504 3242 Planarity : 0.004 0.053 3934 Dihedral : 21.832 179.982 3821 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.05 % Allowed : 22.44 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.67 (0.18), residues: 2286 helix: 1.96 (0.13), residues: 1564 sheet: 2.07 (0.96), residues: 26 loop : -0.93 (0.24), residues: 696 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 482 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 508 average time/residue: 1.0976 time to fit residues: 655.7134 Evaluate side-chains 487 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 461 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 4 average time/residue: 0.6742 time to fit residues: 6.5225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN r 42 ASN e 20 GLN b 42 ASN A 25 GLN f 20 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN g 20 GLN d 20 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23465 Z= 0.256 Angle : 1.170 38.503 32317 Z= 0.462 Chirality : 0.044 0.450 3242 Planarity : 0.004 0.053 3934 Dihedral : 21.792 179.999 3821 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.60 % Allowed : 23.49 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.62 (0.18), residues: 2286 helix: 1.87 (0.13), residues: 1578 sheet: 2.06 (0.95), residues: 26 loop : -0.87 (0.25), residues: 682 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 477 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 26 residues processed: 501 average time/residue: 1.0985 time to fit residues: 648.1603 Evaluate side-chains 486 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 460 time to evaluate : 2.512 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 5 average time/residue: 0.8980 time to fit residues: 8.5257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN o 42 ASN r 42 ASN A 25 GLN J 25 GLN f 20 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.084471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065536 restraints weight = 58231.597| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.21 r_work: 0.2817 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23465 Z= 0.236 Angle : 1.165 38.627 32317 Z= 0.462 Chirality : 0.044 0.413 3242 Planarity : 0.003 0.053 3934 Dihedral : 21.761 179.991 3821 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.80 % Allowed : 23.59 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 1.73 (0.18), residues: 2286 helix: 2.01 (0.13), residues: 1547 sheet: 2.12 (0.94), residues: 26 loop : -0.86 (0.24), residues: 713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9801.97 seconds wall clock time: 173 minutes 48.55 seconds (10428.55 seconds total)