Starting phenix.real_space_refine on Sat Aug 3 12:39:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv4_37864/08_2024/8wv4_37864.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv4_37864/08_2024/8wv4_37864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv4_37864/08_2024/8wv4_37864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv4_37864/08_2024/8wv4_37864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv4_37864/08_2024/8wv4_37864.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv4_37864/08_2024/8wv4_37864.cif" } resolution = 3.3 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= 0.008 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: 5 Type Number sf(0) Gaussians Ca 10 9.91 5 S 20 5.16 5 C 5290 2.51 5 N 1305 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3": "OD1" <-> "OD2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 3": "OD1" <-> "OD2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8170 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} 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: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.06, per 1000 atoms: 0.62 Number of scatterers: 8170 At special positions: 0 Unit cell: (113.42, 115.56, 52.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 10 19.99 S 20 16.00 O 1545 8.00 N 1305 7.00 C 5290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 15 sheets defined 6.8% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 43 through 46 Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'B' and resid 43 through 46 Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'D' and resid 43 through 46 Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 167 through 176 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 39 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 34 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS A 38 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN A 158 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR A 40 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE A 156 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 85 removed outlier: 3.607A pdb=" N SER A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 52 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 55 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 20 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS A 191 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 39 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 34 " --> pdb=" O TRP B 162 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS B 38 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 158 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B 40 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE B 156 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.606A pdb=" N SER B 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 52 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 55 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 20 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 191 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 39 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR C 34 " --> pdb=" O TRP C 162 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS C 38 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN C 158 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR C 40 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE C 156 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 85 removed outlier: 3.607A pdb=" N SER C 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 52 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 55 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 20 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS C 191 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 39 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 34 " --> pdb=" O TRP D 162 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS D 38 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN D 158 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR D 40 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE D 156 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.606A pdb=" N SER D 80 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 52 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 55 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 20 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS D 191 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE E 39 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 34 " --> pdb=" O TRP E 162 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS E 38 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN E 158 " --> pdb=" O HIS E 38 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR E 40 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE E 156 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 80 through 85 removed outlier: 3.606A pdb=" N SER E 80 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE E 52 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA E 55 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 20 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS E 191 " --> pdb=" O LYS E 23 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 735 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: 2.28 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2539 1.34 - 1.46: 2007 1.46 - 1.58: 3814 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 8390 Sorted by residual: bond pdb=" CB ASP D 60 " pdb=" CG ASP D 60 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASP A 60 " pdb=" CG ASP A 60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB ASP C 60 " pdb=" CG ASP C 60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB ASP B 60 " pdb=" CG ASP B 60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CB ASP E 60 " pdb=" CG ASP E 60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 ... (remaining 8385 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 325 107.34 - 114.00: 4608 114.00 - 120.66: 3096 120.66 - 127.32: 3268 127.32 - 133.99: 108 Bond angle restraints: 11405 Sorted by residual: angle pdb=" N GLY C 72 " pdb=" CA GLY C 72 " pdb=" C GLY C 72 " ideal model delta sigma weight residual 110.20 113.10 -2.90 1.32e+00 5.74e-01 4.84e+00 angle pdb=" N GLY D 72 " pdb=" CA GLY D 72 " pdb=" C GLY D 72 " ideal model delta sigma weight residual 110.20 113.10 -2.90 1.32e+00 5.74e-01 4.83e+00 angle pdb=" N GLY B 72 " pdb=" CA GLY B 72 " pdb=" C GLY B 72 " ideal model delta sigma weight residual 110.20 113.09 -2.89 1.32e+00 5.74e-01 4.81e+00 angle pdb=" N GLY E 72 " pdb=" CA GLY E 72 " pdb=" C GLY E 72 " ideal model delta sigma weight residual 110.20 113.09 -2.89 1.32e+00 5.74e-01 4.79e+00 angle pdb=" N GLY A 72 " pdb=" CA GLY A 72 " pdb=" C GLY A 72 " ideal model delta sigma weight residual 110.20 113.08 -2.88 1.32e+00 5.74e-01 4.77e+00 ... (remaining 11400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4525 17.50 - 35.00: 285 35.00 - 52.49: 35 52.49 - 69.99: 20 69.99 - 87.49: 30 Dihedral angle restraints: 4895 sinusoidal: 1940 harmonic: 2955 Sorted by residual: dihedral pdb=" CA PHE A 146 " pdb=" C PHE A 146 " pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE C 146 " pdb=" C PHE C 146 " pdb=" N GLU C 147 " pdb=" CA GLU C 147 " ideal model delta harmonic sigma weight residual -180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE D 146 " pdb=" C PHE D 146 " pdb=" N GLU D 147 " pdb=" CA GLU D 147 " ideal model delta harmonic sigma weight residual -180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 4892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 657 0.025 - 0.049: 312 0.049 - 0.074: 113 0.074 - 0.098: 68 0.098 - 0.123: 85 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CA ILE D 63 " pdb=" N ILE D 63 " pdb=" C ILE D 63 " pdb=" CB ILE D 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE C 63 " pdb=" N ILE C 63 " pdb=" C ILE C 63 " pdb=" CB ILE C 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE A 63 " pdb=" N ILE A 63 " pdb=" C ILE A 63 " pdb=" CB ILE A 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 1232 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 167 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO E 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 167 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO B 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 167 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO A 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.016 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 146 2.53 - 3.12: 5808 3.12 - 3.72: 12054 3.72 - 4.31: 17672 4.31 - 4.90: 30425 Nonbonded interactions: 66105 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" OD1 ASN A 61 " model vdw 1.938 3.040 nonbonded pdb=" OD1 ASP C 60 " pdb=" OD1 ASN C 61 " model vdw 1.939 3.040 nonbonded pdb=" OD1 ASP E 60 " pdb=" OD1 ASN E 61 " model vdw 1.939 3.040 nonbonded pdb=" OD1 ASP B 60 " pdb=" OD1 ASN B 61 " model vdw 1.940 3.040 nonbonded pdb=" OD1 ASP D 60 " pdb=" OD1 ASN D 61 " model vdw 1.940 3.040 ... (remaining 66100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.002 0.037 8390 Z= 0.146 Angle : 0.491 5.980 11405 Z= 0.287 Chirality : 0.044 0.123 1235 Planarity : 0.003 0.029 1450 Dihedral : 14.128 87.489 2990 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.33 % Allowed : 3.33 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.63 (0.23), residues: 1020 helix: 1.99 (0.64), residues: 55 sheet: -1.44 (0.27), residues: 320 loop : -2.37 (0.20), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 110 HIS 0.002 0.001 HIS D 38 PHE 0.009 0.001 PHE B 109 TYR 0.009 0.001 TYR A 54 ARG 0.008 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 0.954 Fit side-chains REVERT: A 101 GLU cc_start: 0.8276 (tt0) cc_final: 0.7927 (tt0) REVERT: A 172 ASN cc_start: 0.8477 (t0) cc_final: 0.8259 (t0) REVERT: A 175 TYR cc_start: 0.8828 (t80) cc_final: 0.8556 (t80) REVERT: B 4 MET cc_start: 0.7729 (mtp) cc_final: 0.7506 (mtp) REVERT: B 62 GLU cc_start: 0.8034 (tp30) cc_final: 0.7804 (tp30) REVERT: B 137 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8086 (mm-40) REVERT: C 62 GLU cc_start: 0.8094 (tp30) cc_final: 0.7863 (tp30) REVERT: C 137 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8004 (mm-40) REVERT: C 175 TYR cc_start: 0.8830 (t80) cc_final: 0.8533 (t80) REVERT: D 62 GLU cc_start: 0.8029 (tp30) cc_final: 0.7267 (tp30) REVERT: D 125 TYR cc_start: 0.8633 (t80) cc_final: 0.7829 (t80) REVERT: D 137 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8190 (mm-40) REVERT: E 62 GLU cc_start: 0.8079 (tp30) cc_final: 0.7846 (tp30) REVERT: E 137 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8067 (mm-40) REVERT: E 172 ASN cc_start: 0.8602 (t0) cc_final: 0.8372 (t0) outliers start: 30 outliers final: 8 residues processed: 245 average time/residue: 0.1916 time to fit residues: 63.4974 Evaluate side-chains 163 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN B 195 GLN C 59 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN D 59 GLN E 59 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8390 Z= 0.470 Angle : 0.609 4.390 11405 Z= 0.340 Chirality : 0.052 0.167 1235 Planarity : 0.005 0.037 1450 Dihedral : 5.069 36.786 1108 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.78 % Allowed : 9.89 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.97 (0.25), residues: 1020 helix: 2.69 (0.67), residues: 55 sheet: -1.11 (0.25), residues: 390 loop : -1.89 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 205 HIS 0.007 0.002 HIS B 38 PHE 0.013 0.002 PHE C 109 TYR 0.021 0.002 TYR D 54 ARG 0.004 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.035 Fit side-chains REVERT: A 101 GLU cc_start: 0.8364 (tt0) cc_final: 0.8031 (tt0) REVERT: A 172 ASN cc_start: 0.8555 (t0) cc_final: 0.8322 (t0) REVERT: A 175 TYR cc_start: 0.9007 (t80) cc_final: 0.8705 (t80) REVERT: A 190 LEU cc_start: 0.9158 (tp) cc_final: 0.8911 (mp) REVERT: B 59 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7795 (tp-100) REVERT: B 137 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8152 (mm-40) REVERT: B 172 ASN cc_start: 0.8557 (t0) cc_final: 0.8346 (t0) REVERT: C 190 LEU cc_start: 0.9175 (tp) cc_final: 0.8948 (mp) REVERT: D 62 GLU cc_start: 0.8486 (tp30) cc_final: 0.8077 (tp30) REVERT: D 125 TYR cc_start: 0.8732 (t80) cc_final: 0.7995 (t80) REVERT: D 137 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8174 (mm-40) REVERT: D 193 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: E 49 TYR cc_start: 0.9093 (p90) cc_final: 0.8812 (p90) REVERT: E 172 ASN cc_start: 0.8660 (t0) cc_final: 0.8437 (t0) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.2040 time to fit residues: 46.2683 Evaluate side-chains 152 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 130 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 195 GLN C 137 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN D 195 GLN E 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8390 Z= 0.166 Angle : 0.498 4.075 11405 Z= 0.277 Chirality : 0.048 0.165 1235 Planarity : 0.003 0.029 1450 Dihedral : 4.059 18.482 1100 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.78 % Allowed : 11.22 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.25), residues: 1020 helix: 2.94 (0.68), residues: 55 sheet: -0.76 (0.32), residues: 280 loop : -1.39 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 162 HIS 0.002 0.001 HIS E 38 PHE 0.008 0.001 PHE A 180 TYR 0.015 0.001 TYR B 54 ARG 0.003 0.000 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 0.990 Fit side-chains REVERT: A 101 GLU cc_start: 0.8234 (tt0) cc_final: 0.7887 (tt0) REVERT: A 172 ASN cc_start: 0.8549 (t0) cc_final: 0.8340 (t0) REVERT: A 175 TYR cc_start: 0.8936 (t80) cc_final: 0.8630 (t80) REVERT: A 190 LEU cc_start: 0.9201 (tp) cc_final: 0.8972 (mp) REVERT: B 137 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7935 (mm-40) REVERT: C 62 GLU cc_start: 0.8530 (tp30) cc_final: 0.8321 (tp30) REVERT: C 190 LEU cc_start: 0.9194 (tp) cc_final: 0.8975 (mp) REVERT: D 16 ASP cc_start: 0.8304 (p0) cc_final: 0.8069 (p0) REVERT: D 62 GLU cc_start: 0.8280 (tp30) cc_final: 0.7773 (tp30) REVERT: D 125 TYR cc_start: 0.8670 (t80) cc_final: 0.7866 (t80) REVERT: E 172 ASN cc_start: 0.8620 (t0) cc_final: 0.8399 (t0) REVERT: E 180 PHE cc_start: 0.8346 (p90) cc_final: 0.7922 (p90) outliers start: 7 outliers final: 3 residues processed: 168 average time/residue: 0.2091 time to fit residues: 47.2327 Evaluate side-chains 150 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 0.0010 chunk 96 optimal weight: 0.0470 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.5686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN B 150 GLN B 195 GLN C 195 GLN D 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8390 Z= 0.159 Angle : 0.480 4.016 11405 Z= 0.267 Chirality : 0.048 0.189 1235 Planarity : 0.003 0.052 1450 Dihedral : 3.850 15.957 1100 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.78 % Allowed : 10.67 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.25), residues: 1020 helix: 2.99 (0.67), residues: 55 sheet: -1.17 (0.33), residues: 230 loop : -0.86 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 162 HIS 0.003 0.001 HIS E 38 PHE 0.009 0.001 PHE D 180 TYR 0.017 0.001 TYR B 54 ARG 0.003 0.000 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 0.994 Fit side-chains REVERT: A 101 GLU cc_start: 0.8233 (tt0) cc_final: 0.7843 (tt0) REVERT: A 172 ASN cc_start: 0.8551 (t0) cc_final: 0.8339 (t0) REVERT: A 175 TYR cc_start: 0.8908 (t80) cc_final: 0.8562 (t80) REVERT: A 190 LEU cc_start: 0.9251 (tp) cc_final: 0.8970 (mp) REVERT: C 186 ASN cc_start: 0.8882 (t0) cc_final: 0.8408 (t0) REVERT: C 190 LEU cc_start: 0.9208 (tp) cc_final: 0.8993 (mp) REVERT: D 16 ASP cc_start: 0.8228 (p0) cc_final: 0.8022 (p0) REVERT: D 62 GLU cc_start: 0.8282 (tp30) cc_final: 0.7784 (tp30) REVERT: D 125 TYR cc_start: 0.8670 (t80) cc_final: 0.7931 (t80) REVERT: E 172 ASN cc_start: 0.8564 (t0) cc_final: 0.8349 (t0) REVERT: E 180 PHE cc_start: 0.8315 (p90) cc_final: 0.7917 (p90) outliers start: 16 outliers final: 14 residues processed: 173 average time/residue: 0.2190 time to fit residues: 51.5840 Evaluate side-chains 159 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN D 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.057 8390 Z= 0.672 Angle : 0.662 4.331 11405 Z= 0.367 Chirality : 0.055 0.289 1235 Planarity : 0.005 0.039 1450 Dihedral : 4.916 26.271 1100 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.00 % Allowed : 11.78 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.25), residues: 1020 helix: 2.89 (0.65), residues: 55 sheet: -0.58 (0.24), residues: 455 loop : -1.79 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 162 HIS 0.006 0.002 HIS D 38 PHE 0.011 0.002 PHE A 66 TYR 0.022 0.003 TYR B 54 ARG 0.003 0.001 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.968 Fit side-chains REVERT: A 101 GLU cc_start: 0.8358 (tt0) cc_final: 0.8094 (tt0) REVERT: A 172 ASN cc_start: 0.8570 (t0) cc_final: 0.8346 (t0) REVERT: A 175 TYR cc_start: 0.9049 (t80) cc_final: 0.8765 (t80) REVERT: B 137 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8231 (mm-40) REVERT: D 62 GLU cc_start: 0.8699 (tp30) cc_final: 0.8330 (tp30) REVERT: D 125 TYR cc_start: 0.8781 (t80) cc_final: 0.8083 (t80) REVERT: E 137 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8158 (mm-40) REVERT: E 172 ASN cc_start: 0.8656 (t0) cc_final: 0.8445 (t0) outliers start: 18 outliers final: 17 residues processed: 152 average time/residue: 0.2112 time to fit residues: 43.2707 Evaluate side-chains 156 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain E residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 195 GLN D 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8390 Z= 0.184 Angle : 0.508 4.241 11405 Z= 0.284 Chirality : 0.049 0.177 1235 Planarity : 0.004 0.053 1450 Dihedral : 4.215 19.976 1100 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.89 % Allowed : 12.33 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.26), residues: 1020 helix: 3.21 (0.66), residues: 55 sheet: -1.00 (0.26), residues: 395 loop : -1.04 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.002 0.001 HIS D 38 PHE 0.009 0.001 PHE A 33 TYR 0.018 0.001 TYR B 54 ARG 0.003 0.000 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 1.028 Fit side-chains REVERT: A 101 GLU cc_start: 0.8239 (tt0) cc_final: 0.7990 (tt0) REVERT: A 172 ASN cc_start: 0.8562 (t0) cc_final: 0.8359 (t0) REVERT: A 175 TYR cc_start: 0.8956 (t80) cc_final: 0.8672 (t80) REVERT: A 190 LEU cc_start: 0.9269 (tp) cc_final: 0.8973 (mp) REVERT: B 38 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.7965 (t70) REVERT: B 137 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8048 (mm-40) REVERT: B 190 LEU cc_start: 0.9210 (tp) cc_final: 0.8972 (mp) REVERT: C 175 TYR cc_start: 0.8964 (t80) cc_final: 0.8644 (t80) REVERT: D 62 GLU cc_start: 0.8503 (tp30) cc_final: 0.8053 (tp30) REVERT: D 125 TYR cc_start: 0.8675 (t80) cc_final: 0.7893 (t80) REVERT: E 172 ASN cc_start: 0.8594 (t0) cc_final: 0.8382 (t0) outliers start: 17 outliers final: 16 residues processed: 159 average time/residue: 0.2204 time to fit residues: 47.0934 Evaluate side-chains 159 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 0.0010 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.0270 overall best weight: 0.5446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN D 195 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8390 Z= 0.167 Angle : 0.501 4.333 11405 Z= 0.278 Chirality : 0.048 0.176 1235 Planarity : 0.003 0.038 1450 Dihedral : 3.964 16.466 1100 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.78 % Allowed : 13.00 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.26), residues: 1020 helix: 3.24 (0.65), residues: 55 sheet: -1.18 (0.27), residues: 335 loop : -0.67 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.004 0.001 HIS E 38 PHE 0.009 0.001 PHE A 33 TYR 0.020 0.001 TYR B 54 ARG 0.003 0.000 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8200 (tt0) cc_final: 0.7966 (tt0) REVERT: A 172 ASN cc_start: 0.8590 (t0) cc_final: 0.8382 (t0) REVERT: A 175 TYR cc_start: 0.8933 (t80) cc_final: 0.8616 (t80) REVERT: A 190 LEU cc_start: 0.9279 (tp) cc_final: 0.8946 (mp) REVERT: B 137 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7901 (mm-40) REVERT: B 190 LEU cc_start: 0.9203 (tp) cc_final: 0.8978 (mp) REVERT: C 175 TYR cc_start: 0.8931 (t80) cc_final: 0.8587 (t80) REVERT: C 186 ASN cc_start: 0.8929 (t0) cc_final: 0.8604 (t0) REVERT: D 62 GLU cc_start: 0.8487 (tp30) cc_final: 0.8012 (tp30) REVERT: D 125 TYR cc_start: 0.8677 (t80) cc_final: 0.7889 (t80) outliers start: 16 outliers final: 13 residues processed: 159 average time/residue: 0.2106 time to fit residues: 44.8614 Evaluate side-chains 157 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8390 Z= 0.232 Angle : 0.513 4.393 11405 Z= 0.287 Chirality : 0.049 0.181 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.028 16.699 1100 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.00 % Allowed : 12.56 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.27), residues: 1020 helix: 3.26 (0.66), residues: 55 sheet: -0.86 (0.27), residues: 395 loop : -0.83 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.003 0.001 HIS E 38 PHE 0.008 0.001 PHE B 33 TYR 0.022 0.002 TYR B 54 ARG 0.003 0.000 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8203 (tt0) cc_final: 0.7961 (tt0) REVERT: A 172 ASN cc_start: 0.8573 (t0) cc_final: 0.8357 (t0) REVERT: A 175 TYR cc_start: 0.8948 (t80) cc_final: 0.8617 (t80) REVERT: A 190 LEU cc_start: 0.9276 (tp) cc_final: 0.8963 (mp) REVERT: B 38 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7897 (t70) REVERT: B 137 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7955 (mm-40) REVERT: B 190 LEU cc_start: 0.9212 (tp) cc_final: 0.8982 (mp) REVERT: D 62 GLU cc_start: 0.8493 (tp30) cc_final: 0.8023 (tp30) REVERT: D 125 TYR cc_start: 0.8681 (t80) cc_final: 0.7902 (t80) outliers start: 18 outliers final: 17 residues processed: 155 average time/residue: 0.2210 time to fit residues: 45.8928 Evaluate side-chains 159 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 0.0670 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8390 Z= 0.156 Angle : 0.490 4.429 11405 Z= 0.272 Chirality : 0.048 0.176 1235 Planarity : 0.003 0.030 1450 Dihedral : 3.799 13.363 1100 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.89 % Allowed : 12.89 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.26), residues: 1020 helix: 3.24 (0.65), residues: 55 sheet: -1.12 (0.28), residues: 335 loop : -0.56 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 162 HIS 0.004 0.001 HIS E 38 PHE 0.010 0.001 PHE A 33 TYR 0.022 0.001 TYR B 54 ARG 0.004 0.000 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8252 (tp30) cc_final: 0.7900 (tp30) REVERT: A 101 GLU cc_start: 0.8161 (tt0) cc_final: 0.7907 (tt0) REVERT: A 125 TYR cc_start: 0.8690 (t80) cc_final: 0.8310 (t80) REVERT: A 172 ASN cc_start: 0.8593 (t0) cc_final: 0.8389 (t0) REVERT: A 175 TYR cc_start: 0.8876 (t80) cc_final: 0.8561 (t80) REVERT: B 137 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7790 (mm-40) REVERT: B 190 LEU cc_start: 0.9219 (tp) cc_final: 0.8996 (mp) REVERT: C 175 TYR cc_start: 0.8890 (t80) cc_final: 0.8548 (t80) REVERT: C 186 ASN cc_start: 0.8921 (t0) cc_final: 0.8596 (t0) REVERT: D 62 GLU cc_start: 0.8338 (tp30) cc_final: 0.7851 (tp30) REVERT: D 125 TYR cc_start: 0.8655 (t80) cc_final: 0.7839 (t80) outliers start: 17 outliers final: 16 residues processed: 167 average time/residue: 0.2212 time to fit residues: 49.2701 Evaluate side-chains 166 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 8390 Z= 0.447 Angle : 0.597 5.424 11405 Z= 0.331 Chirality : 0.052 0.188 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.468 19.536 1100 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.89 % Allowed : 13.44 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.26), residues: 1020 helix: 3.20 (0.65), residues: 55 sheet: -0.94 (0.27), residues: 395 loop : -0.92 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.005 0.002 HIS D 38 PHE 0.010 0.002 PHE E 52 TYR 0.030 0.002 TYR B 125 ARG 0.003 0.001 ARG C 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.976 Fit side-chains REVERT: A 101 GLU cc_start: 0.8289 (tt0) cc_final: 0.7841 (tt0) REVERT: A 172 ASN cc_start: 0.8596 (t0) cc_final: 0.8376 (t0) REVERT: A 190 LEU cc_start: 0.9270 (tp) cc_final: 0.8935 (mp) REVERT: B 137 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8072 (mm-40) REVERT: D 62 GLU cc_start: 0.8593 (tp30) cc_final: 0.8282 (tp30) outliers start: 17 outliers final: 16 residues processed: 151 average time/residue: 0.2128 time to fit residues: 43.2227 Evaluate side-chains 154 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN D 195 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.081915 restraints weight = 12582.721| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.79 r_work: 0.2712 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8390 Z= 0.201 Angle : 0.522 4.962 11405 Z= 0.291 Chirality : 0.049 0.182 1235 Planarity : 0.004 0.061 1450 Dihedral : 4.112 16.821 1100 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.00 % Allowed : 13.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.27), residues: 1020 helix: 3.35 (0.66), residues: 55 sheet: -0.92 (0.27), residues: 395 loop : -0.86 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 162 HIS 0.003 0.001 HIS E 38 PHE 0.009 0.001 PHE A 33 TYR 0.022 0.001 TYR B 54 ARG 0.004 0.000 ARG E 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.03 seconds wall clock time: 34 minutes 39.14 seconds (2079.14 seconds total)