Starting phenix.real_space_refine on Fri Feb 16 18:29:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkg_13471/02_2024/7pkg_13471.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkg_13471/02_2024/7pkg_13471.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/7pkg_13471/02_2024/7pkg_13471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkg_13471/02_2024/7pkg_13471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkg_13471/02_2024/7pkg_13471.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkg_13471/02_2024/7pkg_13471.pdb" } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 10 9.91 5 S 20 5.16 5 C 5290 2.51 5 N 1305 2.21 5 O 1550 1.98 5 H 7980 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 14": "OE1" <-> "OE2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 3": "OD1" <-> "OD2" Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16155 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} 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} 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: "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: "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: "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: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 7.82, per 1000 atoms: 0.48 Number of scatterers: 16155 At special positions: 0 Unit cell: (114.532, 112.86, 53.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 10 19.99 S 20 16.00 O 1550 8.00 N 1305 7.00 C 5290 6.00 H 7980 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 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: 14.58 Conformation dependent library (CDL) restraints added in 2.0 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: 20 helices and 16 sheets defined 12.4% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.852A pdb=" N SER E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 151 Processing helix chain 'E' and resid 167 through 176 Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.990A pdb=" N LEU E 190 " --> pdb=" O TRP E 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.989A pdb=" N SER D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 186 through 190 removed outlier: 4.095A pdb=" N LEU D 190 " --> pdb=" O TRP D 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.791A pdb=" N SER C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 186 through 190 removed outlier: 4.070A pdb=" N LEU C 190 " --> pdb=" O TRP C 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.824A pdb=" N SER B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 186 through 190 removed outlier: 4.009A pdb=" N LEU B 190 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.773A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.958A pdb=" N LEU A 190 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.787A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR E 34 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET E 161 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS E 36 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 159 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 80 through 85 removed outlier: 3.739A pdb=" N TYR E 73 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN E 61 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR E 56 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 139 through 141 removed outlier: 7.066A pdb=" N GLN E 139 " --> pdb=" O PHE E 146 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE E 146 " --> pdb=" O GLN E 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AA6, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.749A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.639A pdb=" N TYR D 73 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN D 61 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR D 56 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.915A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 101 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 85 removed outlier: 3.769A pdb=" N TYR C 73 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN C 61 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR C 56 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AB3, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.776A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.605A pdb=" N TYR B 73 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN B 61 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 56 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB6, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.840A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 101 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 34 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET A 161 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS A 36 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 159 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 80 through 85 removed outlier: 3.610A pdb=" N TYR A 73 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASN A 61 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 56 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 819 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: 6.21 Time building geometry restraints manager: 15.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7980 1.03 - 1.22: 3 1.22 - 1.42: 3615 1.42 - 1.61: 4742 1.61 - 1.80: 30 Bond restraints: 16370 Sorted by residual: bond pdb=" CA PHE B 84 " pdb=" CB PHE B 84 " ideal model delta sigma weight residual 1.528 1.499 0.029 2.61e-02 1.47e+03 1.26e+00 bond pdb=" CB ASN D 186 " pdb=" CG ASN D 186 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CG PRO D 87 " pdb=" CD PRO D 87 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.16e+00 bond pdb=" CB VAL C 91 " pdb=" CG1 VAL C 91 " ideal model delta sigma weight residual 1.521 1.552 -0.031 3.30e-02 9.18e+02 8.72e-01 bond pdb=" CG1 ILE A 82 " pdb=" CD1 ILE A 82 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.50e-01 ... (remaining 16365 not shown) Histogram of bond angle deviations from ideal: 79.78 - 90.64: 42 90.64 - 101.51: 10 101.51 - 112.38: 18545 112.38 - 123.25: 9221 123.25 - 134.11: 1737 Bond angle restraints: 29555 Sorted by residual: angle pdb=" CG2 THR A 46 " pdb=" CB THR A 46 " pdb=" HB THR A 46 " ideal model delta sigma weight residual 108.00 79.78 28.22 3.00e+00 1.11e-01 8.85e+01 angle pdb=" CG2 THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 108.00 80.12 27.88 3.00e+00 1.11e-01 8.64e+01 angle pdb=" OG1 THR A 46 " pdb=" CB THR A 46 " pdb=" HB THR A 46 " ideal model delta sigma weight residual 109.00 81.49 27.51 3.00e+00 1.11e-01 8.41e+01 angle pdb=" CG2 THR A 173 " pdb=" CB THR A 173 " pdb=" HB THR A 173 " ideal model delta sigma weight residual 108.00 80.56 27.44 3.00e+00 1.11e-01 8.37e+01 angle pdb=" CG2 THR E 126 " pdb=" CB THR E 126 " pdb=" HB THR E 126 " ideal model delta sigma weight residual 108.00 80.97 27.03 3.00e+00 1.11e-01 8.12e+01 ... (remaining 29550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 7007 17.49 - 34.98: 494 34.98 - 52.46: 163 52.46 - 69.95: 105 69.95 - 87.44: 16 Dihedral angle restraints: 7785 sinusoidal: 4100 harmonic: 3685 Sorted by residual: dihedral pdb=" CA TYR E 73 " pdb=" C TYR E 73 " pdb=" N SER E 74 " pdb=" CA SER E 74 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU B 62 " pdb=" C GLU B 62 " pdb=" N ILE B 63 " pdb=" CA ILE B 63 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TYR C 73 " pdb=" C TYR C 73 " pdb=" N SER C 74 " pdb=" CA SER C 74 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 7782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 1221 0.348 - 0.696: 0 0.696 - 1.043: 0 1.043 - 1.391: 4 1.391 - 1.739: 10 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CG LEU A 83 " pdb=" CB LEU A 83 " pdb=" CD1 LEU A 83 " pdb=" CD2 LEU A 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.56e+01 chirality pdb=" CG LEU D 43 " pdb=" CB LEU D 43 " pdb=" CD1 LEU D 43 " pdb=" CD2 LEU D 43 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.98e+01 chirality pdb=" CG LEU C 83 " pdb=" CB LEU C 83 " pdb=" CD1 LEU C 83 " pdb=" CD2 LEU C 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.93 -1.66 2.00e-01 2.50e+01 6.90e+01 ... (remaining 1232 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 58 " -0.050 9.50e-02 1.11e+02 4.15e-02 3.27e+01 pdb=" NE ARG B 58 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG B 58 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG B 58 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 58 " 0.079 2.00e-02 2.50e+03 pdb="HH11 ARG B 58 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG B 58 " 0.034 2.00e-02 2.50e+03 pdb="HH21 ARG B 58 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 58 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 188 " -0.083 9.50e-02 1.11e+02 4.07e-02 2.09e+01 pdb=" NE ARG C 188 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 188 " -0.058 2.00e-02 2.50e+03 pdb=" NH1 ARG C 188 " 0.056 2.00e-02 2.50e+03 pdb=" NH2 ARG C 188 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG C 188 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG C 188 " -0.017 2.00e-02 2.50e+03 pdb="HH21 ARG C 188 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 188 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 38 " -0.005 2.00e-02 2.50e+03 2.73e-02 1.86e+01 pdb=" CG HIS E 38 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS E 38 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 HIS E 38 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS E 38 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS E 38 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 HIS E 38 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 HIS E 38 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 HIS E 38 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS E 38 " -0.016 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 752 2.15 - 2.77: 31109 2.77 - 3.38: 46031 3.38 - 3.99: 63656 3.99 - 4.60: 97925 Nonbonded interactions: 239473 Sorted by model distance: nonbonded pdb=" H SER A 167 " pdb=" OE1 GLU A 170 " model vdw 1.543 1.850 nonbonded pdb=" H SER B 167 " pdb=" OE1 GLU B 170 " model vdw 1.565 1.850 nonbonded pdb=" O GLU E 85 " pdb="HH22 ARG E 116 " model vdw 1.565 1.850 nonbonded pdb=" OD1 ASP E 3 " pdb=" HG SER E 5 " model vdw 1.569 1.850 nonbonded pdb=" H SER D 167 " pdb=" OE1 GLU D 170 " model vdw 1.577 1.850 ... (remaining 239468 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' 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: 2.780 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: 0.250 Extract box with map and model: 10.190 Check model and map are aligned: 0.260 Set scattering table: 0.130 Process input model: 58.440 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8390 Z= 0.329 Angle : 0.855 15.383 11405 Z= 0.459 Chirality : 0.166 1.739 1235 Planarity : 0.006 0.080 1450 Dihedral : 13.676 87.441 2990 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.10 (0.24), residues: 1020 helix: -1.53 (0.44), residues: 55 sheet: -0.38 (0.26), residues: 360 loop : -0.82 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.006 TRP E 187 HIS 0.011 0.004 HIS C 38 PHE 0.018 0.003 PHE C 84 TYR 0.023 0.005 TYR E 125 ARG 0.069 0.013 ARG C 188 *********************** 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 95 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.732 Fit side-chains REVERT: E 161 MET cc_start: 0.8031 (ttt) cc_final: 0.7747 (ttt) REVERT: E 186 ASN cc_start: 0.8546 (t0) cc_final: 0.8203 (t0) REVERT: A 83 LEU cc_start: 0.8808 (mt) cc_final: 0.8591 (mt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.6199 time to fit residues: 75.4033 Evaluate side-chains 67 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 ASN B 61 ASN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8390 Z= 0.219 Angle : 0.770 15.784 11405 Z= 0.399 Chirality : 0.167 1.707 1235 Planarity : 0.004 0.053 1450 Dihedral : 6.366 35.785 1100 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.33 % Allowed : 2.67 % Favored : 97.00 % 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: -0.66 (0.24), residues: 1020 helix: 0.86 (0.51), residues: 55 sheet: -0.26 (0.23), residues: 420 loop : -0.63 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 110 HIS 0.006 0.002 HIS A 38 PHE 0.015 0.002 PHE E 66 TYR 0.025 0.002 TYR E 54 ARG 0.005 0.001 ARG E 188 *********************** 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 86 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.412 Fit side-chains REVERT: E 161 MET cc_start: 0.8164 (ttt) cc_final: 0.7893 (ttt) REVERT: E 186 ASN cc_start: 0.8485 (t0) cc_final: 0.8030 (t0) REVERT: D 186 ASN cc_start: 0.8573 (t0) cc_final: 0.8370 (t0) REVERT: C 197 GLU cc_start: 0.7344 (tt0) cc_final: 0.7065 (pp20) REVERT: A 18 SER cc_start: 0.8857 (m) cc_final: 0.8423 (p) outliers start: 3 outliers final: 1 residues processed: 86 average time/residue: 0.5186 time to fit residues: 60.4115 Evaluate side-chains 72 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR 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: 1.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN A 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8390 Z= 0.227 Angle : 0.741 15.734 11405 Z= 0.382 Chirality : 0.167 1.723 1235 Planarity : 0.004 0.063 1450 Dihedral : 5.667 26.021 1100 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.44 % Allowed : 4.00 % Favored : 95.56 % 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: -0.51 (0.25), residues: 1020 helix: 2.24 (0.63), residues: 55 sheet: -0.34 (0.22), residues: 445 loop : -0.50 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 110 HIS 0.007 0.002 HIS A 38 PHE 0.011 0.001 PHE E 66 TYR 0.023 0.001 TYR E 54 ARG 0.007 0.000 ARG A 58 *********************** 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 83 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.349 Fit side-chains REVERT: E 161 MET cc_start: 0.8260 (ttt) cc_final: 0.7987 (ttt) REVERT: D 18 SER cc_start: 0.8885 (m) cc_final: 0.8472 (p) REVERT: C 180 PHE cc_start: 0.8521 (p90) cc_final: 0.8251 (p90) REVERT: A 18 SER cc_start: 0.8849 (m) cc_final: 0.8641 (p) outliers start: 4 outliers final: 1 residues processed: 83 average time/residue: 0.5070 time to fit residues: 56.3909 Evaluate side-chains 71 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8390 Z= 0.221 Angle : 0.731 16.409 11405 Z= 0.374 Chirality : 0.168 1.797 1235 Planarity : 0.003 0.040 1450 Dihedral : 5.302 18.195 1100 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.56 % Allowed : 5.56 % Favored : 93.89 % 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: -0.43 (0.25), residues: 1020 helix: 2.75 (0.68), residues: 55 sheet: -0.38 (0.22), residues: 445 loop : -0.42 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 162 HIS 0.006 0.002 HIS B 38 PHE 0.011 0.001 PHE B 52 TYR 0.019 0.001 TYR E 54 ARG 0.005 0.000 ARG B 58 *********************** 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 82 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 1.521 Fit side-chains REVERT: C 180 PHE cc_start: 0.8501 (p90) cc_final: 0.8152 (p90) outliers start: 5 outliers final: 2 residues processed: 81 average time/residue: 0.5002 time to fit residues: 55.8637 Evaluate side-chains 68 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain D residue 80 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8390 Z= 0.301 Angle : 0.737 16.365 11405 Z= 0.378 Chirality : 0.167 1.735 1235 Planarity : 0.004 0.036 1450 Dihedral : 5.295 17.742 1100 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.78 % Allowed : 6.78 % Favored : 92.44 % 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: -0.54 (0.25), residues: 1020 helix: 2.60 (0.67), residues: 55 sheet: -0.43 (0.22), residues: 445 loop : -0.52 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 162 HIS 0.006 0.002 HIS E 38 PHE 0.014 0.002 PHE E 52 TYR 0.020 0.001 TYR E 54 ARG 0.002 0.000 ARG D 58 *********************** 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 76 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.399 Fit side-chains REVERT: D 18 SER cc_start: 0.8887 (m) cc_final: 0.8468 (p) REVERT: A 180 PHE cc_start: 0.8611 (p90) cc_final: 0.8347 (p90) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.4738 time to fit residues: 49.2172 Evaluate side-chains 70 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 173 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8390 Z= 0.218 Angle : 0.721 16.276 11405 Z= 0.368 Chirality : 0.167 1.727 1235 Planarity : 0.003 0.032 1450 Dihedral : 5.140 16.447 1100 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.44 % Allowed : 8.33 % Favored : 91.22 % 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: -0.49 (0.25), residues: 1020 helix: 2.76 (0.67), residues: 55 sheet: -0.43 (0.22), residues: 445 loop : -0.46 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 162 HIS 0.005 0.002 HIS E 38 PHE 0.011 0.001 PHE E 52 TYR 0.016 0.001 TYR E 54 ARG 0.002 0.000 ARG D 58 *********************** 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 73 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.525 Fit side-chains REVERT: D 18 SER cc_start: 0.8875 (m) cc_final: 0.8494 (p) REVERT: A 180 PHE cc_start: 0.8578 (p90) cc_final: 0.8320 (p90) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.4985 time to fit residues: 49.7882 Evaluate side-chains 68 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain A residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8390 Z= 0.216 Angle : 0.713 16.276 11405 Z= 0.365 Chirality : 0.164 1.727 1235 Planarity : 0.003 0.033 1450 Dihedral : 5.012 15.957 1100 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.44 % Allowed : 8.89 % Favored : 90.67 % 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: -0.45 (0.25), residues: 1020 helix: 2.80 (0.67), residues: 55 sheet: -0.40 (0.22), residues: 445 loop : -0.44 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 162 HIS 0.006 0.002 HIS E 38 PHE 0.010 0.001 PHE E 52 TYR 0.016 0.001 TYR E 54 ARG 0.004 0.000 ARG B 58 *********************** 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 72 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.476 Fit side-chains REVERT: E 161 MET cc_start: 0.8335 (ttt) cc_final: 0.7948 (ttt) REVERT: D 18 SER cc_start: 0.8863 (m) cc_final: 0.8509 (p) REVERT: A 180 PHE cc_start: 0.8574 (p90) cc_final: 0.8288 (p90) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.4865 time to fit residues: 47.5334 Evaluate side-chains 69 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain A residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8390 Z= 0.195 Angle : 0.708 16.231 11405 Z= 0.361 Chirality : 0.165 1.729 1235 Planarity : 0.003 0.034 1450 Dihedral : 4.901 15.464 1100 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.33 % Allowed : 9.22 % Favored : 90.44 % 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: -0.35 (0.25), residues: 1020 helix: 2.91 (0.67), residues: 55 sheet: -0.34 (0.23), residues: 445 loop : -0.36 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 162 HIS 0.006 0.002 HIS E 38 PHE 0.011 0.001 PHE B 180 TYR 0.014 0.001 TYR E 54 ARG 0.003 0.000 ARG B 58 *********************** 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 75 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 161 MET cc_start: 0.8312 (ttt) cc_final: 0.7935 (ttt) REVERT: D 18 SER cc_start: 0.8862 (m) cc_final: 0.8515 (p) REVERT: A 180 PHE cc_start: 0.8577 (p90) cc_final: 0.8281 (p90) outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 0.4899 time to fit residues: 50.1861 Evaluate side-chains 74 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain A residue 166 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8390 Z= 0.333 Angle : 0.734 16.456 11405 Z= 0.378 Chirality : 0.165 1.739 1235 Planarity : 0.004 0.034 1450 Dihedral : 5.081 17.472 1100 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.44 % Allowed : 9.44 % Favored : 90.11 % 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: -0.58 (0.25), residues: 1020 helix: 2.45 (0.66), residues: 55 sheet: -0.38 (0.23), residues: 420 loop : -0.60 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.005 0.002 HIS A 38 PHE 0.016 0.002 PHE E 52 TYR 0.020 0.002 TYR E 54 ARG 0.002 0.000 ARG B 58 *********************** 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 69 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.626 Fit side-chains revert: symmetry clash REVERT: D 18 SER cc_start: 0.8879 (m) cc_final: 0.8528 (p) REVERT: A 180 PHE cc_start: 0.8621 (p90) cc_final: 0.8303 (p90) outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.5201 time to fit residues: 49.1977 Evaluate side-chains 67 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain D residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8390 Z= 0.207 Angle : 0.710 16.217 11405 Z= 0.363 Chirality : 0.164 1.724 1235 Planarity : 0.003 0.033 1450 Dihedral : 4.931 16.281 1100 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.33 % Allowed : 9.78 % Favored : 89.89 % 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: -0.43 (0.25), residues: 1020 helix: 2.78 (0.67), residues: 55 sheet: -0.34 (0.23), residues: 420 loop : -0.48 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 162 HIS 0.006 0.002 HIS E 38 PHE 0.010 0.001 PHE D 39 TYR 0.013 0.001 TYR E 54 ARG 0.003 0.000 ARG B 58 ********************** 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 80 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 18 SER cc_start: 0.8891 (m) cc_final: 0.8548 (p) REVERT: C 28 LYS cc_start: 0.8118 (mttt) cc_final: 0.7835 (mmmt) REVERT: A 180 PHE cc_start: 0.8584 (p90) cc_final: 0.8306 (p90) outliers start: 3 outliers final: 3 residues processed: 80 average time/residue: 0.5277 time to fit residues: 56.7571 Evaluate side-chains 76 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain A residue 166 LEU 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: 0.5980 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.077337 restraints weight = 35864.085| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.57 r_work: 0.2728 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8390 Z= 0.206 Angle : 0.708 16.234 11405 Z= 0.361 Chirality : 0.165 1.727 1235 Planarity : 0.003 0.035 1450 Dihedral : 4.854 15.916 1100 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.33 % Allowed : 9.78 % Favored : 89.89 % 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: -0.39 (0.25), residues: 1020 helix: 2.83 (0.67), residues: 55 sheet: -0.37 (0.23), residues: 445 loop : -0.39 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.005 0.002 HIS E 38 PHE 0.010 0.001 PHE E 52 TYR 0.014 0.001 TYR E 54 ARG 0.003 0.000 ARG B 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.96 seconds wall clock time: 71 minutes 22.05 seconds (4282.05 seconds total)