Starting phenix.real_space_refine on Fri Feb 16 18:24:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkb_13467/02_2024/7pkb_13467.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkb_13467/02_2024/7pkb_13467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkb_13467/02_2024/7pkb_13467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkb_13467/02_2024/7pkb_13467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkb_13467/02_2024/7pkb_13467.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkb_13467/02_2024/7pkb_13467.pdb" } resolution = 3.2 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 7970 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 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ASP 70": "OD1" <-> "OD2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 197": "OE1" <-> "OE2" 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 81": "OE1" <-> "OE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C TYR 49": "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 GLU 62": "OE1" <-> "OE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 3": "OD1" <-> "OD2" 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 PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 49": "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 GLU 108": "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 ASP 169": "OD1" <-> "OD2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16145 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 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: 7.26, per 1000 atoms: 0.45 Number of scatterers: 16145 At special positions: 0 Unit cell: (113.696, 115.368, 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 7970 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=2.04 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=2.04 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: 13.57 Conformation dependent library (CDL) restraints added in 1.9 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 15 sheets defined 12.1% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'E' and resid 42 through 46 removed outlier: 4.037A pdb=" N SER E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 176 Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.996A pdb=" N LEU E 190 " --> pdb=" O TRP E 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 removed outlier: 4.019A 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 176 Processing helix chain 'D' and resid 186 through 190 removed outlier: 4.073A pdb=" N LEU D 190 " --> pdb=" O TRP D 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 4.050A 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 176 Processing helix chain 'C' and resid 186 through 190 removed outlier: 4.004A pdb=" N LEU C 190 " --> pdb=" O TRP C 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 4.040A 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 176 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.987A pdb=" N LEU B 190 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.248A 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 176 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.856A 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: 3.513A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR E 34 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET E 161 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS E 36 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL E 159 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.009A 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: 3.507A pdb=" N TYR E 73 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.571A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.183A pdb=" N ASN D 61 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR D 56 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (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: 3.525A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.073A 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: 3.631A pdb=" N TYR C 73 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN C 61 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR C 56 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.539A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.520A pdb=" N TYR B 73 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASN B 61 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR B 56 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB5, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.551A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR A 34 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET A 161 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N CYS A 36 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 159 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 80 through 85 removed outlier: 6.176A pdb=" N ASN A 61 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR A 56 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 810 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: 6.25 Time building geometry restraints manager: 13.95 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: 7970 1.03 - 1.22: 0 1.22 - 1.41: 3613 1.41 - 1.61: 4747 1.61 - 1.80: 30 Bond restraints: 16360 Sorted by residual: bond pdb=" CB THR D 98 " pdb=" CG2 THR D 98 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.87e+00 bond pdb=" CB VAL D 94 " pdb=" CG1 VAL D 94 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB VAL E 94 " pdb=" CG1 VAL E 94 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" CB THR B 76 " pdb=" CG2 THR B 76 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.16e+00 bond pdb=" CB VAL C 94 " pdb=" CG1 VAL C 94 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 ... (remaining 16355 not shown) Histogram of bond angle deviations from ideal: 79.83 - 90.69: 30 90.69 - 101.55: 11 101.55 - 112.41: 18578 112.41 - 123.27: 9200 123.27 - 134.13: 1716 Bond angle restraints: 29535 Sorted by residual: angle pdb=" CG1 VAL A 77 " pdb=" CB VAL A 77 " pdb=" HB VAL A 77 " ideal model delta sigma weight residual 108.00 79.83 28.17 3.00e+00 1.11e-01 8.81e+01 angle pdb=" CG2 VAL A 77 " pdb=" CB VAL A 77 " pdb=" HB VAL A 77 " ideal model delta sigma weight residual 108.00 80.17 27.83 3.00e+00 1.11e-01 8.61e+01 angle pdb=" CG2 ILE A 82 " pdb=" CB ILE A 82 " pdb=" HB ILE A 82 " ideal model delta sigma weight residual 109.00 81.65 27.35 3.00e+00 1.11e-01 8.31e+01 angle pdb=" CG1 VAL E 77 " pdb=" CB VAL E 77 " pdb=" HB VAL E 77 " ideal model delta sigma weight residual 108.00 80.70 27.30 3.00e+00 1.11e-01 8.28e+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 80.75 27.25 3.00e+00 1.11e-01 8.25e+01 ... (remaining 29530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7037 17.99 - 35.98: 453 35.98 - 53.97: 179 53.97 - 71.96: 99 71.96 - 89.95: 7 Dihedral angle restraints: 7775 sinusoidal: 4100 harmonic: 3675 Sorted by residual: dihedral pdb=" CA GLU C 62 " pdb=" C GLU C 62 " pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+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 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA GLU E 62 " pdb=" C GLU E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 7772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 1225 0.349 - 0.698: 0 0.698 - 1.047: 0 1.047 - 1.395: 5 1.395 - 1.744: 5 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.61e+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 -0.90 -1.69 2.00e-01 2.50e+01 7.16e+01 chirality pdb=" CB VAL B 89 " pdb=" CA VAL B 89 " pdb=" CG1 VAL B 89 " pdb=" CG2 VAL B 89 " both_signs ideal model delta sigma weight residual False -2.63 -1.08 -1.55 2.00e-01 2.50e+01 5.98e+01 ... (remaining 1232 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 183 " -0.032 2.00e-02 2.50e+03 4.02e-02 2.42e+01 pdb=" CG ASN E 183 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN E 183 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN E 183 " 0.065 2.00e-02 2.50e+03 pdb="HD21 ASN E 183 " 0.001 2.00e-02 2.50e+03 pdb="HD22 ASN E 183 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 86 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO B 87 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 183 " 0.028 2.00e-02 2.50e+03 3.49e-02 1.82e+01 pdb=" CG ASN D 183 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN D 183 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 183 " -0.057 2.00e-02 2.50e+03 pdb="HD21 ASN D 183 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN D 183 " 0.053 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 625 2.14 - 2.76: 30525 2.76 - 3.37: 45052 3.37 - 3.99: 63257 3.99 - 4.60: 96940 Nonbonded interactions: 236399 Sorted by model distance: nonbonded pdb=" HG1 THR B 41 " pdb=" O VAL B 153 " model vdw 1.531 1.850 nonbonded pdb=" HG1 THR C 41 " pdb=" O VAL C 153 " model vdw 1.541 1.850 nonbonded pdb=" OE1 GLU A 101 " pdb=" HG SER A 104 " model vdw 1.545 1.850 nonbonded pdb="HH22 ARG E 47 " pdb=" O SER E 151 " model vdw 1.556 1.850 nonbonded pdb=" HG1 THR A 41 " pdb=" O VAL A 153 " model vdw 1.557 1.850 ... (remaining 236394 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: 5.510 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: 0.260 Extract box with map and model: 10.610 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 54.510 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.008 0.056 8390 Z= 0.518 Angle : 0.903 14.543 11405 Z= 0.500 Chirality : 0.142 1.744 1235 Planarity : 0.006 0.110 1450 Dihedral : 13.281 89.946 2990 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.80 % 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: -0.98 (0.24), residues: 1020 helix: -1.59 (0.49), residues: 55 sheet: -0.19 (0.23), residues: 425 loop : -0.86 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.006 TRP A 67 HIS 0.007 0.003 HIS D 95 PHE 0.018 0.003 PHE D 109 TYR 0.025 0.005 TYR D 54 ARG 0.063 0.012 ARG E 6 *********************** 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 93 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.331 Fit side-chains REVERT: D 60 ASP cc_start: 0.7358 (p0) cc_final: 0.7086 (p0) REVERT: C 81 GLU cc_start: 0.7682 (tt0) cc_final: 0.7373 (tt0) REVERT: C 163 ASP cc_start: 0.7947 (p0) cc_final: 0.7715 (p0) REVERT: A 60 ASP cc_start: 0.7556 (p0) cc_final: 0.7051 (p0) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.6105 time to fit residues: 72.9287 Evaluate side-chains 75 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 0.0070 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 1 GLN E 38 HIS C 95 HIS B 95 HIS A 95 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1201 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= 0.213 Angle : 0.711 15.251 11405 Z= 0.372 Chirality : 0.141 1.705 1235 Planarity : 0.004 0.061 1450 Dihedral : 6.087 28.806 1100 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.33 % Allowed : 2.11 % Favored : 97.56 % 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: -0.25 (0.25), residues: 1020 helix: 1.48 (0.62), residues: 55 sheet: 0.21 (0.23), residues: 425 loop : -0.60 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 162 HIS 0.004 0.002 HIS D 38 PHE 0.015 0.001 PHE E 66 TYR 0.021 0.001 TYR C 54 ARG 0.006 0.001 ARG B 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 90 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 1.464 Fit side-chains REVERT: D 60 ASP cc_start: 0.7482 (p0) cc_final: 0.7116 (p0) REVERT: C 81 GLU cc_start: 0.7705 (tt0) cc_final: 0.7344 (tt0) REVERT: A 60 ASP cc_start: 0.7534 (p0) cc_final: 0.7009 (p0) outliers start: 3 outliers final: 3 residues processed: 90 average time/residue: 0.6762 time to fit residues: 76.2894 Evaluate side-chains 78 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain A residue 134 ILE 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: 0.4980 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: 1.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 0.0870 chunk 89 optimal weight: 0.5980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 HIS D 59 GLN D 95 HIS D 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1775 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= 0.193 Angle : 0.665 15.598 11405 Z= 0.345 Chirality : 0.141 1.698 1235 Planarity : 0.003 0.038 1450 Dihedral : 5.316 20.582 1100 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.22 % Allowed : 3.67 % Favored : 96.11 % 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: 0.02 (0.26), residues: 1020 helix: 2.24 (0.64), residues: 55 sheet: 0.36 (0.24), residues: 415 loop : -0.44 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 162 HIS 0.008 0.001 HIS E 38 PHE 0.008 0.001 PHE D 52 TYR 0.019 0.001 TYR C 54 ARG 0.003 0.000 ARG B 188 *********************** 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 88 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.428 Fit side-chains REVERT: D 147 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6773 (mt-10) REVERT: A 60 ASP cc_start: 0.7582 (p0) cc_final: 0.7024 (p0) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.6735 time to fit residues: 74.3402 Evaluate side-chains 79 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain A residue 134 ILE 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: 0.7980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1971 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 : 0.662 15.540 11405 Z= 0.343 Chirality : 0.141 1.696 1235 Planarity : 0.004 0.062 1450 Dihedral : 5.173 20.340 1100 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.44 % Allowed : 5.11 % Favored : 94.44 % 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: -0.06 (0.26), residues: 1020 helix: 2.14 (0.62), residues: 55 sheet: 0.29 (0.24), residues: 415 loop : -0.48 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 162 HIS 0.008 0.002 HIS E 38 PHE 0.010 0.001 PHE D 66 TYR 0.018 0.001 TYR E 54 ARG 0.006 0.000 ARG A 188 *********************** 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 81 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.434 Fit side-chains REVERT: D 147 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 60 ASP cc_start: 0.7564 (p0) cc_final: 0.7086 (p0) outliers start: 4 outliers final: 3 residues processed: 81 average time/residue: 0.7020 time to fit residues: 70.6810 Evaluate side-chains 78 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain A residue 134 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.0010 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2195 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= 0.185 Angle : 0.643 15.414 11405 Z= 0.332 Chirality : 0.141 1.699 1235 Planarity : 0.003 0.046 1450 Dihedral : 4.924 18.963 1100 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.22 % Allowed : 5.56 % Favored : 94.22 % 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: -0.02 (0.27), residues: 1020 helix: 2.25 (0.63), residues: 55 sheet: 0.26 (0.25), residues: 415 loop : -0.41 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 162 HIS 0.006 0.001 HIS E 38 PHE 0.009 0.001 PHE D 39 TYR 0.015 0.001 TYR C 54 ARG 0.004 0.000 ARG A 188 *********************** 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 86 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.531 Fit side-chains REVERT: D 147 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6743 (mt-10) REVERT: A 60 ASP cc_start: 0.7647 (p0) cc_final: 0.7094 (p0) outliers start: 2 outliers final: 1 residues processed: 86 average time/residue: 0.7357 time to fit residues: 80.0059 Evaluate side-chains 80 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8390 Z= 0.297 Angle : 0.672 15.659 11405 Z= 0.350 Chirality : 0.142 1.702 1235 Planarity : 0.004 0.049 1450 Dihedral : 5.150 23.082 1100 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.44 % Allowed : 5.78 % Favored : 93.78 % 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: -0.30 (0.26), residues: 1020 helix: 1.79 (0.61), residues: 55 sheet: 0.13 (0.25), residues: 415 loop : -0.61 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 162 HIS 0.007 0.002 HIS E 38 PHE 0.012 0.002 PHE D 66 TYR 0.019 0.001 TYR E 54 ARG 0.005 0.001 ARG C 188 *********************** 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 79 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 1.486 Fit side-chains REVERT: A 60 ASP cc_start: 0.7671 (p0) cc_final: 0.7117 (p0) outliers start: 4 outliers final: 2 residues processed: 79 average time/residue: 0.6788 time to fit residues: 67.2152 Evaluate side-chains 74 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain A residue 134 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8390 Z= 0.245 Angle : 0.657 15.562 11405 Z= 0.340 Chirality : 0.141 1.701 1235 Planarity : 0.004 0.051 1450 Dihedral : 5.082 23.069 1100 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.33 % Allowed : 6.44 % Favored : 93.22 % 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: -0.37 (0.26), residues: 1020 helix: 1.86 (0.62), residues: 55 sheet: 0.06 (0.25), residues: 415 loop : -0.66 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.006 0.002 HIS E 38 PHE 0.010 0.001 PHE D 39 TYR 0.015 0.001 TYR C 54 ARG 0.006 0.001 ARG C 188 *********************** 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 80 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.450 Fit side-chains REVERT: A 60 ASP cc_start: 0.7675 (p0) cc_final: 0.7149 (p0) outliers start: 3 outliers final: 2 residues processed: 80 average time/residue: 0.6843 time to fit residues: 68.8731 Evaluate side-chains 75 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain A residue 134 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2514 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= 0.169 Angle : 0.634 15.473 11405 Z= 0.326 Chirality : 0.141 1.693 1235 Planarity : 0.004 0.054 1450 Dihedral : 4.811 19.633 1100 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.11 % Allowed : 6.67 % Favored : 93.22 % 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: -0.23 (0.27), residues: 1020 helix: 2.15 (0.63), residues: 55 sheet: 0.11 (0.25), residues: 415 loop : -0.54 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.005 0.001 HIS E 38 PHE 0.012 0.001 PHE D 39 TYR 0.013 0.001 TYR C 54 ARG 0.007 0.000 ARG C 188 *********************** 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 81 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.413 Fit side-chains REVERT: C 81 GLU cc_start: 0.7540 (tt0) cc_final: 0.7239 (tt0) REVERT: A 60 ASP cc_start: 0.7655 (p0) cc_final: 0.7094 (p0) outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.6714 time to fit residues: 68.0469 Evaluate side-chains 78 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE 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: 0.5980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.0370 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8390 Z= 0.238 Angle : 0.650 15.614 11405 Z= 0.336 Chirality : 0.141 1.697 1235 Planarity : 0.004 0.058 1450 Dihedral : 4.921 20.878 1100 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.11 % Allowed : 6.78 % Favored : 93.11 % 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: -0.35 (0.27), residues: 1020 helix: 1.93 (0.62), residues: 55 sheet: 0.02 (0.25), residues: 415 loop : -0.60 (0.27), residues: 550 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 D 39 TYR 0.015 0.001 TYR E 54 ARG 0.006 0.001 ARG C 188 *********************** 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 80 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.446 Fit side-chains REVERT: C 81 GLU cc_start: 0.7553 (tt0) cc_final: 0.7238 (tt0) REVERT: A 60 ASP cc_start: 0.7582 (p0) cc_final: 0.7029 (p0) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.6927 time to fit residues: 69.5154 Evaluate side-chains 80 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.0470 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.0270 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2673 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= 0.167 Angle : 0.629 15.456 11405 Z= 0.323 Chirality : 0.141 1.692 1235 Planarity : 0.004 0.056 1450 Dihedral : 4.682 17.697 1100 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.00 % 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: -0.19 (0.27), residues: 1020 helix: 2.24 (0.63), residues: 55 sheet: 0.08 (0.25), residues: 415 loop : -0.46 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.005 0.001 HIS E 38 PHE 0.011 0.001 PHE D 39 TYR 0.012 0.001 TYR C 54 ARG 0.007 0.000 ARG C 188 ********************** 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 85 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.345 Fit side-chains REVERT: A 60 ASP cc_start: 0.7647 (p0) cc_final: 0.7081 (p0) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.6669 time to fit residues: 71.1915 Evaluate side-chains 79 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE 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: 0.4980 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.079861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.064378 restraints weight = 38472.783| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 2.53 r_work: 0.2464 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2316 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2646 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= 0.222 Angle : 0.644 15.581 11405 Z= 0.332 Chirality : 0.141 1.699 1235 Planarity : 0.004 0.055 1450 Dihedral : 4.802 19.683 1100 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % 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: -0.31 (0.27), residues: 1020 helix: 2.06 (0.62), residues: 55 sheet: 0.02 (0.25), residues: 415 loop : -0.56 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 162 HIS 0.005 0.002 HIS E 38 PHE 0.010 0.001 PHE D 39 TYR 0.014 0.001 TYR E 54 ARG 0.006 0.000 ARG C 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4195.71 seconds wall clock time: 74 minutes 47.55 seconds (4487.55 seconds total)